Binding Site Information of Target
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T81503 | Target Info | |||
| Target Name | Bacterial DNA gyrase B (Bact gyrB) | ||||
| Synonyms | gyrB; DNA gyrase subunit B | ||||
| Target Type | Clinical trial Target | ||||
| Gene Name | Bact gyrB | ||||
| Biochemical Class | ATP-hydrolyzing DNA topoisomerase | ||||
| UniProt ID | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: Novobiocin | Ligand Info | |||||
| Structure Description | NOVOBIOCIN-RESISTANT MUTANT (R136H) OF THE N-TERMINAL 24 KDA FRAGMENT OF DNA GYRASE B COMPLEXED WITH NOVOBIOCIN AT 2.3 ANGSTROMS RESOLUTION | PDB:1AJ6 | ||||
| Method | X-ray diffraction | Resolution | 2.30 Å | Mutation | Yes | [1] |
| PDB Sequence |
VLKGLDAVRK
21 RPGMYIGDTD31 DGTGLHHMVF41 EVVDNAIDEA51 LAGHCKEIIV61 TIHADNSVSV 71 QDDGRGIPTG81 IVSAAEVIMT96 VLHAGGKFSG113 GLHGVGVSVV123 NALSQKLELV 133 IQHEGKIHRQ143 IYEHGVPQAP153 LAVTGETEKT163 GTMVRFWPSL173 ETFTNVTEFE 183 YEILAKRLRE193 LSFLNSGVSI203 RLRDKRDGKE213 DHFH
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| Ligand Name: Salicylamide | Ligand Info | |||||
| Structure Description | E. coli GyrB ATPase domain in complex with 2-hydroxybenzamide | PDB:7DQH | ||||
| Method | X-ray diffraction | Resolution | 1.91 Å | Mutation | No | [2] |
| PDB Sequence |
LDAVRKRPGM
25 YIGDTDDGTG35 LHHMVFEVVD45 NAIDEALAGH55 CKEIIVTIHA65 DNSVSVQDDG 75 RGIPTGIHPE85 EGVSAAEVIM95 TVLGVGVSVV123 NALSQKLELV133 IQREGKIHRQ 143 IYEHGVPQAP153 LAVTGETEKT163 GTMVRFWPSL173 ETFTNVTEFE183 YEILAKRLRE 193 LSFLNSGVSI203 RLRDKRDGKE213 DHFHY
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| Ligand Name: adenosine diphosphate | Ligand Info | |||||
| Structure Description | E. coli GyrB 43-kDa N-terminal fragment in complex with ADP+Pi | PDB:4PRX | ||||
| Method | X-ray diffraction | Resolution | 1.80 Å | Mutation | No | [3] |
| PDB Sequence |
SYDSSSIKVL
13 KGLDAVRKRP23 GMYIGDTDDG33 TGLHHMVFEV43 VDNAIDEALA53 GHCKEIIVTI 63 HADNSVSVQD73 DGRGIPTGIH83 PEEGVSAAEV93 IMTVLHAGGK103 FDDNSYKVSG 113 GLHGVGVSVV123 NALSQKLELV133 IQREGKIHRQ143 IYEHGVPQAP153 LAVTGETEKT 163 GTMVRFWPSL173 ETFTNVTEFE183 YEILAKRLRE193 LSFLNSGVSI203 RLRDKRDGKE 213 DHFHYEGGIK223 AFVEYLNKNK233 TPIHPNIFYF243 STEKDGIGVE253 VALQWNDGFQ 263 ENIYCFTNNI273 PQRDGGTHLA283 GFRAAMTRTL293 NAYMDKEGYS303 AREGLIAVVS 324 VKVPDPKFSS334 QTKDKLVSSE344 VKSAVEQQMN354 ELLAEYLLEN364 PTDAKIVVGK 374 IID
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .ADP or .ADP2 or .ADP3 or :3ADP;style chemicals stick;color identity;select .A:43 or .A:46 or .A:47 or .A:49 or .A:50 or .A:73 or .A:75 or .A:76 or .A:77 or .A:78 or .A:79 or .A:94 or .A:100 or .A:101 or .A:102 or .A:103 or .A:108 or .A:109 or .A:114 or .A:115 or .A:116 or .A:117 or .A:118 or .A:119 or .A:120 or .A:121 or .A:165 or .A:167 or .A:337; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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VAL43
4.474
ASN46
1.981
ALA47
3.277
ASP49
4.802
GLU50
2.882
ASP73
1.846
GLY75
4.983
ARG76
3.552
GLY77
3.348
ILE78
2.678
PRO79
3.385
ILE94
2.391
ALA100
2.884
GLY101
2.172
GLY102
1.998
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: AMP-PNP | Ligand Info | |||||
| Structure Description | N-terminal 43 kDa fragment of the E. coli DNA gyrase B subunit grown from 100 mM KCl condition | PDB:4WUB | ||||
| Method | X-ray diffraction | Resolution | 1.75 Å | Mutation | No | [4] |
| PDB Sequence |
SYDSSSIKVL
13 KGLDAVRKRP23 GMYIGDTDDG33 TGLHHMVFEV43 VDNAIDEALA53 GHCKEIIVTI 63 HADNSVSVQD73 DGRGIPTGIH83 PEEGVSAAEV93 IMTVLHAGGK103 FDDNSYKVSG 113 GLHGVGVSVV123 NALSQKLELV133 IQREGKIHRQ143 IYEHGVPQAP153 LAVTGETEKT 163 GTMVRFWPSL173 ETFTNVTEFE183 YEILAKRLRE193 LSFLNSGVSI203 RLRDKRDGKE 213 DHFHYEGGIK223 AFVEYLNKNK233 TPIHPNIFYF243 STEKDGIGVE253 VALQWNDGFQ 263 ENIYCFTNNI273 PQRDGGTHLA283 GFRAAMTRTL293 NAYMDKEGYS303 SATGDDAREG 318 LIAVVSVKVP328 DPKFSSQTKD338 KLVSSEVKSA348 VEQQMNELLA358 EYLLENPTDA 368 KIVVGKIIDA378 ARAREAARRA388 REMT
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .ANP or .ANP2 or .ANP3 or :3ANP;style chemicals stick;color identity;select .A:42 or .A:46 or .A:47 or .A:49 or .A:50 or .A:73 or .A:77 or .A:78 or .A:79 or .A:94 or .A:100 or .A:101 or .A:102 or .A:103 or .A:109 or .A:113 or .A:114 or .A:115 or .A:116 or .A:117 or .A:118 or .A:119 or .A:120 or .A:121 or .A:165 or .A:335 or .A:337; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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GLU42
3.574
ASN46
2.881
ALA47
4.212
ASP49
4.755
GLU50
3.228
ASP73
2.799
GLY77
3.895
ILE78
3.403
PRO79
4.730
ILE94
3.251
ALA100
3.490
GLY101
3.672
GLY102
2.871
LYS103
2.838
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 2-Chlorophenol | Ligand Info | |||||
| Structure Description | E. coli GyrB ATPase domain in complex with 2-chlorophenol | PDB:7DQS | ||||
| Method | X-ray diffraction | Resolution | 1.85 Å | Mutation | No | [2] |
| PDB Sequence |
LDAVRKRPGM
25 YIGDTDDGTG35 LHHMVFEVVD45 NAIDEALAGH55 CKEIIVTIHA65 DNSVSVQDDG 75 RGIPTGIHPE85 EGVSAAEVIM95 TVLVGVSVVN124 ALSQKLELVI134 QREGKIHRQI 144 YEHGVPQAPL154 AVTGETEKTG164 TMVRFWPSLE174 TFTNVTEFEY184 EILAKRLREL 194 SFLNSGVSIR204 LRDKRDGKED214 HFHY
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .2CH or .2CH2 or .2CH3 or :32CH;style chemicals stick;color identity;select .A:43 or .A:46 or .A:47 or .A:50 or .A:71 or .A:72 or .A:73 or .A:78 or .A:120 or .A:165 or .A:166 or .A:167; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: Methyl p-hydroxybenzoate | Ligand Info | |||||
| Structure Description | E. coli GyrB ATPase domain in complex with methyl 4-hydroxybenzoate | PDB:7DQU | ||||
| Method | X-ray diffraction | Resolution | 1.88 Å | Mutation | No | [2] |
| PDB Sequence |
LDAVRKRPGM
25 YIGDTDDGTG35 LHHMVFEVVD45 NAIDEALAGH55 CKEIIVTIHA65 DNSVSVQDDG 75 RGIPTGIHPE85 EGVSAAEVIM95 TVLGVGVSVV123 NALSQKLELV133 IQREGKIHRQ 143 IYEHGVPQAP153 LAVTGETEKT163 GTMVRFWPSL173 ETFTNVTEFE183 YEILAKRLRE 193 LSFLNSGVSI203 RLRDKRDGKE213 DHFHY
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .MPB or .MPB2 or .MPB3 or :3MPB;style chemicals stick;color identity;select .A:43 or .A:46 or .A:47 or .A:50 or .A:71 or .A:72 or .A:73 or .A:78 or .A:94 or .A:95 or .A:120 or .A:165 or .A:166 or .A:167; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: Esculetin | Ligand Info | |||||
| Structure Description | E. coli GyrB ATPase domain in complex with Esculetin | PDB:7DQI | ||||
| Method | X-ray diffraction | Resolution | 1.91 Å | Mutation | No | [2] |
| PDB Sequence |
LDAVRKRPGM
25 YIGDTDDGTG35 LHHMVFEVVD45 NAIDEALAGH55 CKEIIVTIHA65 DNSVSVQDDG 75 RGIPTGIHPE85 EGVSAAEVIM95 TVLGVGVSVV123 NALSQKLELV133 IQREGKIHRQ 143 IYEHGVPQAP153 LAVTGETEKT163 GTMVRFWPSL173 ETFTNVTEFE183 YEILAKRLRE 193 LSFLNSGVSI203 RLRDKRDGKE213 DHFHY
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .HFC or .HFC2 or .HFC3 or :3HFC;style chemicals stick;color identity;select .A:43 or .A:46 or .A:47 or .A:50 or .A:71 or .A:72 or .A:73 or .A:78 or .A:94 or .A:95 or .A:120 or .A:165 or .A:166 or .A:167; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: Clorobiocin | Ligand Info | |||||
| Structure Description | Crystal Structure of E. coli 24kDa Domain in Complex with Clorobiocin | PDB:1KZN | ||||
| Method | X-ray diffraction | Resolution | 2.30 Å | Mutation | No | [5] |
| PDB Sequence |
GLDAVRKRPG
24 MYIGDTDDGT34 GLHHMVFEVV44 DNAIDEALAG54 HCKEIIVTIH64 ADNSVSVQDD 74 GRGIPTGIGV84 SAAEVIMTVL94 HAHGVGVSVV123 NALSQKLELV133 IQREGKIHRQ 143 IYEHGVPQAP153 LAVTGETEKT163 GTMVRFWPSL173 ETFTNVTEFE183 YEILAKRLRE 193 LSFLNSGVSI203 RLRDKRDGKE213 DHFHYE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .CBN or .CBN2 or .CBN3 or :3CBN;style chemicals stick;color identity;select .A:43 or .A:46 or .A:47 or .A:49 or .A:50 or .A:71 or .A:72 or .A:73 or .A:76 or .A:77 or .A:78 or .A:79 or .A:86 or .A:90 or .A:91 or .A:120 or .A:136 or .A:165 or .A:166 or .A:167; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 2-[[2-[[4,5-Bis(Bromanyl)-1~{h}-Pyrrol-2-Yl]carbonylamino]-1,3-Benzothiazol-6-Yl]amino]-2-Oxidanylidene-Ethanoic Acid | Ligand Info | |||||
| Structure Description | ESCHERICHIA COLI DNA GYRASE B IN COMPLEX WITH BENZOTHIAZOLE-BASED INHIBITOR | PDB:5L3J | ||||
| Method | X-ray diffraction | Resolution | 2.83 Å | Mutation | No | [6] |
| PDB Sequence |
GLDAVRKRPG
24 MYIGDTDDGT34 GLHHMVFEVV44 DNAIDEALAG54 HCKEIIVTIH64 ADNSVSVQDD 74 GRGIPTGIHP84 EEGVSAAEVI94 MTVLHVGVSV122 VNALSQKLEL132 VIQREGKIHR 142 QIYEHGVPQA152 PLAVTGETEK162 TGTMVRFWPS172 LETFTNVTEF182 EYEILAKRLR 192 ELSFLNSGVS202 IRLRDKRDGK212 EDHFHYEGGI222 KAFVEYLNKN232 KTPIHPNIFY 242 FSTEKDGIGV252 EVALQWNDGF262 QENIYCFTNN272 IPQRDGGTHL282 AGFRAAMTRT 292 LNAYMDKEGY302 SKKAKVSATG312 DDAREGLIAV322 VSVKVPDPKF332 SSQTKDKLVS 342 SEVKSAVEQQ352 MNELLAEYLL362 ENPTDAKIVV372 GKIIDAARAR382 EAARRAREMT 392
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .6G9 or .6G92 or .6G93 or :36G9;style chemicals stick;color identity;select .A:43 or .A:46 or .A:47 or .A:50 or .A:55 or .A:71 or .A:73 or .A:76 or .A:77 or .A:78 or .A:79 or .A:95 or .A:120 or .A:136 or .A:165 or .A:166 or .A:167; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 6-(ethylcarbamoylamino)-4-pyrazol-1-yl-~{N}-pyridin-3-yl-pyridine-3-carboxamide | Ligand Info | |||||
| Structure Description | Crystal Structure of E. coli GyraseB 24kDa in complex with 6-[(ethylcarbamoyl)amino]-4-(1H-pyrazol-1-yl)-N-(pyridin-3-yl)pyridine-3-carboxamide | PDB:6F8J | ||||
| Method | X-ray diffraction | Resolution | 1.95 Å | Mutation | No | [7] |
| PDB Sequence |
GLDAVRKRPG
24 MYIGDTDDGT34 GLHHMVFEVV44 DNAIDEALAG54 HCKEIIVTIH64 ADNSVSVQDD 74 GRGIPTGIHP84 EEGVSAAEVI94 MTVLGVGVSV122 VNALSQKLEL132 VIQREGKIHR 142 QIYEHGVPQA152 PLAVTGETEK162 TGTMVRFWPS172 LETFTNVTEF182 EYEILAKRLR 192 ELSFLNSGVS202 IRLRDKRDGK212 EDHFHYE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .CZ5 or .CZ52 or .CZ53 or :3CZ5;style chemicals stick;color identity;select .A:43 or .A:46 or .A:47 or .A:50 or .A:71 or .A:72 or .A:73 or .A:76 or .A:77 or .A:78 or .A:79 or .A:94 or .A:136 or .A:165 or .A:166 or .A:167; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 6-(ethylcarbamoylamino)-~{N}-(3-methylphenyl)-4-[(3-methylphenyl)amino]pyridine-3-carboxamide | Ligand Info | |||||
| Structure Description | Crystal Structure of E. coli GyraseB 24kDa in complex with 6-[(ethylcarbamoyl)amino]-4-[(3-methyphenyl)amino]-N-(3-methyphenyl)pyridine-3-carboxamide | PDB:6F94 | ||||
| Method | X-ray diffraction | Resolution | 2.35 Å | Mutation | No | [7] |
| PDB Sequence |
GLDAVRKRPG
24 MYIGDTDDGT34 GLHHMVFEVV44 DNAIDEALAG54 HCKEIIVTIH64 ADNSVSVQDD 74 GRGIPTGIHP84 EEGVSAAEVI94 MTVLGVGVSV122 VNALSQKLEL132 VIQREGKIHR 142 QIYEHGVPQA152 PLAVTGETEK162 TGTMVRFWPS172 LETFTNVTEF182 EYEILAKRLR 192 ELSFLNSGVS202 IRLRDKRDGK212 EDHFHYE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .D0H or .D0H2 or .D0H3 or :3D0H;style chemicals stick;color identity;select .A:43 or .A:46 or .A:47 or .A:50 or .A:71 or .A:72 or .A:73 or .A:76 or .A:77 or .A:78 or .A:79 or .A:94 or .A:136 or .A:165 or .A:166 or .A:167; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 2-[[3,4-bis(chloranyl)-5-methyl-1H-pyrrol-2-yl]carbonylamino]-5-oxidanyl-1,3-benzothiazole-6-carboxylic acid | Ligand Info | |||||
| Structure Description | E.coli GyrB24 with inhibitor LSJ38 (EBL2684) | PDB:7P2N | ||||
| Method | X-ray diffraction | Resolution | 1.16 Å | Mutation | No | [8] |
| PDB Sequence |
SIKVLKGLDA
18 VRKRPGMYIG28 DTDDGTGLHH38 MVFEVVDNAI48 DEALAGHCKE58 IIVTIHADNS 68 VSVQDDGRGI78 PTGIHPEEGV88 SAAEVIMTVL98 GVGVSVVNAL126 SQKLELVIQR 136 EGKIHRQIYE146 HGVPQAPLAV156 TGETEKTGTM166 VRFWPSLETF176 TNVTEFEYEI 186 LAKRLRELSF196 LNSGVSIRLR206 DKRDGKEDHF216 HY
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .4R3 or .4R32 or .4R33 or :34R3;style chemicals stick;color identity;select .A:43 or .A:46 or .A:47 or .A:50 or .A:71 or .A:73 or .A:76 or .A:77 or .A:78 or .A:79 or .A:94 or .A:120 or .A:136 or .A:165 or .A:167; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 2-[[3,4-bis(chloranyl)-5-methyl-1~{H}-pyrrol-2-yl]carbonylamino]-4-phenylmethoxy-1,3-benzothiazole-6-carboxylic acid | Ligand Info | |||||
| Structure Description | E.coli GyrB24 with inhibitor LMD43 (EBL2560) | PDB:7P2M | ||||
| Method | X-ray diffraction | Resolution | 1.16 Å | Mutation | No | [9] |
| PDB Sequence |
SSIKVLKGLD
17 AVRKRPGMYI27 GDTDDGTGLH37 HMVFEVVDNA47 IDEALAGHCK57 EIIVTIHADN 67 SVSVQDDGRG77 IPTGIHPEEG87 VSAAEVIMTV97 LGVGVSVVNA125 LSQKLELVIQ 135 REGKIHRQIY145 EHGVPQAPLA155 VTGETEKTGT165 MVRFWPSLET175 FTNVTEFEYE 185 ILAKRLRELS195 FLNSGVSIRL205 RDKRDGKEDH215 FHY
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .N1N or .N1N2 or .N1N3 or :3N1N;style chemicals stick;color identity;select .A:43 or .A:46 or .A:47 or .A:50 or .A:71 or .A:73 or .A:76 or .A:77 or .A:78 or .A:79 or .A:94 or .A:120 or .A:136 or .A:165 or .A:167; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 4-{[4'-Methyl-2'-(propanoylamino)-4,5'-bi-1,3-thiazol-2-yl]amino}benzoic acid | Ligand Info | |||||
| Structure Description | Crystal structure of 24 kDa domain of E. coli DNA gyrase B in complex with small molecule inhibitor | PDB:4DUH | ||||
| Method | X-ray diffraction | Resolution | 1.50 Å | Mutation | No | [10] |
| PDB Sequence |
GLDAVRKRPG
24 MYIGDTDDGT34 GLHHMVFEVV44 DNAIDEALAG54 HCKEIIVTIH64 ADNSVSVQDD 74 GRGIPTGIHP84 EEGVSAAEVI94 MTVLHAGGKF104 DDNSGVGVSV122 VNALSQKLEL 132 VIQREGKIHR142 QIYEHGVPQA152 PLAVTGETEK162 TGTMVRFWPS172 LETFTNVTEF 182 EYEILAKRLR192 ELSFLNSGVS202 IRLRDKRDGK212 EDHFH
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .RLI or .RLI2 or .RLI3 or :3RLI;style chemicals stick;color identity;select .A:43 or .A:46 or .A:47 or .A:50 or .A:71 or .A:73 or .A:76 or .A:77 or .A:78 or .A:79 or .A:94 or .A:100 or .A:101 or .A:103 or .A:120 or .A:136 or .A:165 or .A:166 or .A:167; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: N-[6-(3-azanylpropanoylamino)-1,3-benzothiazol-2-yl]-3,4-bis(chloranyl)-5-methyl-1H-pyrrole-2-carboxamide | Ligand Info | |||||
| Structure Description | Ecoli GyrB24 with inhibitor 16a | PDB:6YD9 | ||||
| Method | X-ray diffraction | Resolution | 1.60 Å | Mutation | No | [11] |
| PDB Sequence |
SYDSSSIKVL
13 KGLDAVRKRP23 GMYIGDTDDG33 TGLHHMVFEV43 VDNAIDEALA53 GHCKEIIVTI 63 HADNSVSVQD73 DGRGIPTGIH83 PEEGVSAAEV93 IMTVLHGVGV120 SVVNALSQKL 130 ELVIQREGKI140 HRQIYEHGVP150 QAPLAVTGET160 EKTGTMVRFW170 PSLETFTNVT 180 EFEYEILAKR190 LRELSFLNSG200 VSIRLRDKRD210 GKEDHFHY
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .ON2 or .ON22 or .ON23 or :3ON2;style chemicals stick;color identity;select .A:43 or .A:46 or .A:47 or .A:50 or .A:71 or .A:73 or .A:76 or .A:77 or .A:78 or .A:79 or .A:94 or .A:120 or .A:136 or .A:165 or .A:167; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 2-[[3,4-bis(chloranyl)-5-methyl-1H-pyrrol-2-yl]carbonylamino]-4-[(3-carboxyphenyl)methoxy]-1,3-benzothiazole-6-carboxylic acid | Ligand Info | |||||
| Structure Description | E.coli GyrB24 with inhibitor LMD92 (EBL2682) | PDB:7P2W | ||||
| Method | X-ray diffraction | Resolution | 1.65 Å | Mutation | No | [12] |
| PDB Sequence |
KGLDAVRKRP
23 GMYIGDTDDG33 TGLHHMVFEV43 VDNAIDEALA53 GHCKEIIVTI63 HADNSVSVQD 73 DGRGIPTGIH83 PEEGVSAAEV93 IMTVLHAGGK103 FDDNSYKVGL115 HGVGVSVVNA 125 LSQKLELVIQ135 REGKIHRQIY145 EHGVPQAPLA155 VTGETEKTGT165 MVRFWPSLET 175 FTNVTEFEYE185 ILAKRLRELS195 FLNSGVSIRL205 RDKRDGKEDH215 FHYE |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .4QR or .4QR2 or .4QR3 or :34QR;style chemicals stick;color identity;select .A:43 or .A:46 or .A:47 or .A:50 or .A:71 or .A:73 or .A:76 or .A:77 or .A:78 or .A:79 or .A:94 or .A:100 or .A:101 or .A:117 or .A:118 or .A:120 or .A:136 or .A:165 or .A:167; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 4-[[4-(3-azanylpropylamino)-6-fluoranyl-8-(methylamino)-2-oxidanylidene-1~{H}-quinolin-3-yl]carbonylamino]benzoic acid | Ligand Info | |||||
| Structure Description | Crystal structure of E.coli DNA gyrase B in complex with 6-fluoro-8-(methylamino)-2-oxo-1,2-dihydroquinoline derivative | PDB:7C7O | ||||
| Method | X-ray diffraction | Resolution | 1.80 Å | Mutation | No | [13] |
| PDB Sequence |
SSSIKVLKGL
16 DAVRKRPGMY26 IGDTDDGTGL36 HHMVFEVVDN46 AIDEALAGHC56 KEIIVTIHAD 66 NSVSVQDDGR76 GIPTGIHPEE86 GVSAAEVIMT96 VLHHGVGVSV122 VNALSQKLEL 132 VIQREGKIHR142 QIYEHGVPQA152 PLAVTGETEK162 TGTMVRFWPS172 LETFTNVTEF 182 EYEILAKRLR192 ELSFLNSGVS202 IRLRDKRDGK212 EDHFHY
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .FKU or .FKU2 or .FKU3 or :3FKU;style chemicals stick;color identity;select .A:43 or .A:46 or .A:47 or .A:49 or .A:50 or .A:71 or .A:72 or .A:73 or .A:76 or .A:77 or .A:78 or .A:79 or .A:94 or .A:95 or .A:120 or .A:136 or .A:165 or .A:166 or .A:167; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: Type II topoisomerase inhibitor 1 | Ligand Info | |||||
| Structure Description | Crystal structure of E.coli DNA gyrase B in complex with 2-oxo-1,2-dihydroquinoline derivative | PDB:6KZZ | ||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [14] |
| PDB Sequence |
DSSSIKVLKG
15 LDAVRKRPGM25 YIGDTDDGTG35 LHHMVFEVVD45 NAIDEALAGH55 CKEIIVTIHA 65 DNSVSVQDDG75 RGIPTGIHPE85 EGVSAAEVIM95 TVLHVGVSVV123 NALSQKLELV 133 IQREGKIHRQ143 IYEHGVPQAP153 LAVTGETEKT163 GTMVRFWPSL173 ETFTNVTEFE 183 YEILAKRLRE193 LSFLNSGVSI203 RLRDKRDGKE213 DHFHYE
|
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .E0R or .E0R2 or .E0R3 or :3E0R;style chemicals stick;color identity;select .A:43 or .A:46 or .A:47 or .A:50 or .A:71 or .A:72 or .A:73 or .A:76 or .A:77 or .A:78 or .A:79 or .A:94 or .A:95 or .A:120 or .A:136 or .A:165 or .A:166 or .A:167; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| Ligand Name: 3-[[8-(methylamino)-2-oxidanylidene-1~{H}-quinolin-3-yl]carbonylamino]benzoic acid | Ligand Info | |||||
| Structure Description | Crystal structure of E.coli DNA gyrase B in complex with 2-oxo-1,2-dihydroquinoline derivative | PDB:6KZX | ||||
| Method | X-ray diffraction | Resolution | 2.10 Å | Mutation | No | [14] |
| PDB Sequence |
SSSIKVLKGL
16 DAVRKRPGMY26 IGDTDDGTGL36 HHMVFEVVDN46 AIDEALAGHC56 KEIIVTIHAD 66 NSVSVQDDGR76 GIPTGIHPEE86 GVSAAEVIMT96 VLHLHGVGVS121 VVNALSQKLE 131 LVIQREGKIH141 RQIYEHGVPQ151 APLAVTGETE161 KTGTMVRFWP171 SLETFTNVTE 181 FEYEILAKRL191 RELSFLNSGV201 SIRLRDKRDG211 KEDHFHYE
|
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .E0L or .E0L2 or .E0L3 or :3E0L;style chemicals stick;color identity;select .A:43 or .A:46 or .A:47 or .A:50 or .A:71 or .A:72 or .A:73 or .A:76 or .A:77 or .A:78 or .A:79 or .A:94 or .A:95 or .A:120 or .A:136 or .A:165 or .A:166 or .A:167; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| Ligand Name: 4-[[6-fluoranyl-8-(methylamino)-2-oxidanylidene-1~{H}-quinolin-3-yl]carbonylamino]benzoic acid | Ligand Info | |||||
| Structure Description | Crystal structure of E.coli DNA gyrase B in complex with 6-fluoro-8-(methylamino)-2-oxo-1,2-dihydroquinoline derivative | PDB:7C7N | ||||
| Method | X-ray diffraction | Resolution | 2.30 Å | Mutation | No | [13] |
| PDB Sequence |
SSSIKVLKGL
16 DAVRKRPGMY26 IGDTDDGTGL36 HHMVFEVVDN46 AIDEALAGHC56 KEIIVTIHAD 66 NSVSVQDDGR76 GIPTGIHPEE86 GVSAAEVIMT96 VLHGLHGVGV120 SVVNALSQKL 130 ELVIQREGKI140 HRQIYEHGVP150 QAPLAVTGET160 EKTGTMVRFW170 PSLETFTNVT 180 EFEYEILAKR190 LRELSFLNSG200 VSIRLRDKRD210 GKEDHFHY
|
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .FKR or .FKR2 or .FKR3 or :3FKR;style chemicals stick;color identity;select .A:43 or .A:46 or .A:47 or .A:50 or .A:71 or .A:72 or .A:73 or .A:76 or .A:77 or .A:78 or .A:79 or .A:94 or .A:95 or .A:120 or .A:136 or .A:165 or .A:166 or .A:167; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| Ligand Name: N-[2-[[cyclohexyl(methyl)amino]methyl]phenyl]-2-oxo-1H-quinoline-3-carboxamide | Ligand Info | |||||
| Structure Description | Crystal structure of E.coli DNA gyrase B in complex with 2-oxo-1,2-dihydroquinoline derivative | PDB:6KZV | ||||
| Method | X-ray diffraction | Resolution | 2.40 Å | Mutation | No | [14] |
| PDB Sequence |
DSSSIKVLKG
15 LDAVRKRPGM25 YIGDTDDGTG35 LHHMVFEVVD45 NAIDEALAGH55 CKEIIVTIHA 65 DNSVSVQDDG75 RGIPTGIHPE85 EGVSAAEVIM95 TVLHAVGVSV122 VNALSQKLEL 132 VIQREGKIHR142 QIYEHGVPQA152 PLAVTGETEK162 TGTMVRFWPS172 LETFTNVTEF 182 EYEILAKRLR192 ELSFLNSGVS202 IRLRDKRDGK212 EDHFHYEG
|
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .E0F or .E0F2 or .E0F3 or :3E0F;style chemicals stick;color identity;select .A:43 or .A:46 or .A:47 or .A:50 or .A:73 or .A:76 or .A:77 or .A:78 or .A:79 or .A:94 or .A:95 or .A:100 or .A:120 or .A:136 or .A:165 or .A:167; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 2-[3-[[8-(methylamino)-2-oxidanylidene-1~{H}-quinolin-3-yl]carbonylamino]phenyl]ethanoic acid | Ligand Info | |||||
| Structure Description | Crystal structure of E.coli DNA gyrase B in complex with 2-oxo-1,2-dihydroquinoline derivative | PDB:6L01 | ||||
| Method | X-ray diffraction | Resolution | 2.60 Å | Mutation | No | [14] |
| PDB Sequence |
SSSIKVLKGL
16 DAVRKRPGMY26 IGDTDDGTGL36 HHMVFEVVDN46 AIDEALAGHC56 KEIIVTIHAD 66 NSVSVQDDGR76 GIPTGIHPEE86 GVSAAEVIMT96 VLHGVGVSVV123 NALSQKLELV 133 IQREGKIHRQ143 IYEHGVPQAP153 LAVTGETEKT163 GTMVRFWPSL173 ETFTNVTEFE 183 YEILAKRLRE193 LSFLNSGVSI203 RLRDKRDGKE213 DHFHYE
|
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .E0U or .E0U2 or .E0U3 or :3E0U;style chemicals stick;color identity;select .A:43 or .A:46 or .A:47 or .A:50 or .A:71 or .A:72 or .A:73 or .A:76 or .A:77 or .A:78 or .A:79 or .A:94 or .A:95 or .A:120 or .A:136 or .A:165 or .A:166 or .A:167; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| Ligand Name: 6-Fluoro-4-[(3ar,6ar)-Hexahydropyrrolo[3,4-B]pyrrol-5(1h)-Yl]-N-Methyl-2-[(2-Methylpyrimidin-5-Yl)oxy]-9h-Pyrimido[4,5-B]indol-8-Amine | Ligand Info | |||||
| Structure Description | The DNA Gyrase B ATP binding domain of Escherichia coli in complex with a small molecule inhibitor. | PDB:4KFG | ||||
| Method | X-ray diffraction | Resolution | 1.60 Å | Mutation | No | [15] |
| PDB Sequence |
GLDAVRKRPG
24 MYIGDTDDGT34 GLHHMVFEVV44 DNAIDEALAG54 HCKEIIVTIH64 ADNSVSVQDD 74 GRGIPTGIVS85 AAEVIMTVLK110 VSGGLHGVGV120 SVVNALSQKL130 ELVIQREGKI 140 HRQIYEHGVP150 QAPLAVTGET160 EKTGTMVRFW170 PSLETFTNVT180 EFEYEILAKR 190 LRELSFLNSG200 VSIRLRDKRD210 GKEDHFHYE
|
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .DOO or .DOO2 or .DOO3 or :3DOO;style chemicals stick;color identity;select .A:43 or .A:46 or .A:47 or .A:49 or .A:50 or .A:71 or .A:72 or .A:73 or .A:76 or .A:77 or .A:78 or .A:79 or .A:90 or .A:91 or .A:120 or .A:136 or .A:165 or .A:166 or .A:167; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| Ligand Name: N-[7-(1h-Imidazol-1-Yl)-2-(Pyridin-3-Yl)[1,3]thiazolo[5,4-D]pyrimidin-5-Yl]cyclopropanecarboxamide | Ligand Info | |||||
| Structure Description | Pyrrolopyrimidine inhibitors of dna gyrase b and topoisomerase iv, part i: structure guided discovery and optimization of dual targeting agents with potent, broad-spectrum enzymatic activity. | PDB:4HYP | ||||
| Method | X-ray diffraction | Resolution | 2.60 Å | Mutation | No | [16] |
| PDB Sequence |
GLDAVRKRPG
24 MYIGDTDDGT34 GLHHMVFEVV44 DNAIDEALAG54 HCKEIIVTIH64 ADNSVSVQDD 74 GRGIPTGIVS89 AAEVIMTVLH99 AGGKFKVSGG118 LHGVGVSVVN128 ALSQKLELVI 138 QREGKIHRQI148 YEHGVPQAPL158 AVTGETEKTG168 TMVRFWPSLE178 TFTNVTEFEY 188 EILAKRLREL198 SFLNSGVSIR208 LRDKRDGKED218 HFHY
|
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .1A1 or .1A12 or .1A13 or :31A1;style chemicals stick;color identity;select .A:43 or .A:44 or .A:46 or .A:47 or .A:50 or .A:71 or .A:73 or .A:76 or .A:77 or .A:78 or .A:79 or .A:94 or .A:101 or .A:104 or .A:124 or .A:140 or .A:169 or .A:170 or .A:171; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| Ligand Name: 2-Fluoro-4-hydroxybenzonitrile | Ligand Info | |||||
| Structure Description | Bacterial GyrB ATPase domain in complex with a chemical fragment | PDB:5Z9L | ||||
| Method | X-ray diffraction | Resolution | 1.60 Å | Mutation | No | [17] |
| PDB Sequence |
LDAVRKRPGM
25 YIGDTDDGTG35 LHHMVFEVVD45 NAIDEALAGH55 CKEIIVTIHA65 DNSVSVQDDG 75 RGIPTGIHPE85 EGVSAAEVIM95 TVLGVGVSVV123 NALSQKLELV133 IQREGKIHRQ 143 IYEHGVPQAP153 LAVTGETEKT163 GTMVRFWPSL173 ETFTNVTEFE183 YEILAKRLRE 193 LSFLNSGVSI203 RLRDKRDGKE213 DHFHYE
|
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .8H8 or .8H82 or .8H83 or :38H8;style chemicals stick;color identity;select .A:43 or .A:46 or .A:47 or .A:50 or .A:71 or .A:72 or .A:73 or .A:78 or .A:94 or .A:95 or .A:120 or .A:165 or .A:166 or .A:167; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| Ligand Name: 2-Aminobenzimidazole | Ligand Info | |||||
| Structure Description | Bacterial GyrB ATPase domain in complex with a chemical fragment | PDB:5Z4O | ||||
| Method | X-ray diffraction | Resolution | 1.73 Å | Mutation | No | [17] |
| PDB Sequence |
LDAVRKRPGM
25 YIGDTDDGTG35 LHHMVFEVVD45 NAIDEALAGH55 CKEIIVTIHA65 DNSVSVQDDG 75 RGIPTGIHPE85 EGVSAAEVIM95 TVLVGVSVVN124 ALSQKLELVI134 QREGKIHRQI 144 YEHGVPQAPL154 AVTGETEKTG164 TMVRFWPSLE174 TFTNVTEFEY184 EILAKRLREL 194 SFLNSGVSIR204 LRDKRDGKED214 HFHY
|
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .AX7 or .AX72 or .AX73 or :3AX7;style chemicals stick;color identity;select .A:20 or .A:147 or .A:149 or .A:174; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 4-Phenoxyphenol | Ligand Info | |||||
| Structure Description | Bacterial GyrB ATPase domain in complex with a chemical fragment | PDB:5Z4O | ||||
| Method | X-ray diffraction | Resolution | 1.73 Å | Mutation | No | [17] |
| PDB Sequence |
LDAVRKRPGM
25 YIGDTDDGTG35 LHHMVFEVVD45 NAIDEALAGH55 CKEIIVTIHA65 DNSVSVQDDG 75 RGIPTGIHPE85 EGVSAAEVIM95 TVLVGVSVVN124 ALSQKLELVI134 QREGKIHRQI 144 YEHGVPQAPL154 AVTGETEKTG164 TMVRFWPSLE174 TFTNVTEFEY184 EILAKRLREL 194 SFLNSGVSIR204 LRDKRDGKED214 HFHY
|
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .HX8 or .HX82 or .HX83 or :3HX8;style chemicals stick;color identity;select .A:43 or .A:46 or .A:47 or .A:50 or .A:71 or .A:72 or .A:73 or .A:78 or .A:91 or .A:94 or .A:95 or .A:120 or .A:132 or .A:134 or .A:165 or .A:166 or .A:167; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| Ligand Name: 2-Hydroxybenzonitrile | Ligand Info | |||||
| Structure Description | Bacterial GyrB ATPase domain in complex with a chemical fragment | PDB:5Z9F | ||||
| Method | X-ray diffraction | Resolution | 1.76 Å | Mutation | No | [17] |
| PDB Sequence |
LDAVRKRPGM
25 YIGDTDDGTG35 LHHMVFEVVD45 NAIDEALAGH55 CKEIIVTIHA65 DNSVSVQDDG 75 RGIPTGIHPE85 EGVSAAEVIM95 TVLGVGVSVV123 NALSQKLELV133 IQREGKIHRQ 143 IYEHGVPQAP153 LAVTGETEKT163 GTMVRFWPSL173 ETFTNVTEFE183 YEILAKRLRE 193 LSFLNSGVSI203 RLRDKRDGKE213 DHFHY
|
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .0R0 or .0R02 or .0R03 or :30R0;style chemicals stick;color identity;select .A:43 or .A:46 or .A:47 or .A:50 or .A:71 or .A:73 or .A:78 or .A:94 or .A:95 or .A:120 or .A:165 or .A:166 or .A:167; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 3-Phenyl-1H-pyrazol-5-amine | Ligand Info | |||||
| Structure Description | Bacterial GyrB ATPase domain in complex with a chemical fragment | PDB:5Z9Q | ||||
| Method | X-ray diffraction | Resolution | 1.80 Å | Mutation | No | [17] |
| PDB Sequence |
LDAVRKRPGM
25 YIGDTDDGTG35 LHHMVFEVVD45 NAIDKEIIVT62 IHADNSVSVQ72 DDGRGIPTGI 82 HPEEGVSAAE92 VIMTVLGVGV120 SVVNALSQKL130 ELVIQREGKI140 HRQIYEHGVP 150 QAPLAVTGET160 EKTGTMVRFW170 PSLETFTNVT180 EFEYEILAKR190 LRELSFLNSG 200 VSIRLRDKRD210 GKEDHFHY
|
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .HX4 or .HX42 or .HX43 or :3HX4;style chemicals stick;color identity;select .A:43 or .A:46 or .A:47 or .A:71 or .A:72 or .A:73 or .A:78 or .A:94 or .A:120 or .A:165 or .A:166 or .A:167; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| Ligand Name: Butylparaben | Ligand Info | |||||
| Structure Description | Bacterial GyrB ATPase domain in complex with a chemical fragment | PDB:5Z9E | ||||
| Method | X-ray diffraction | Resolution | 1.80 Å | Mutation | No | [17] |
| PDB Sequence |
LDAVRKRPGM
25 YIGDTDDGTG35 LHHMVFEVVD45 NAIDEALAGH55 CKEIIVTIHA65 DNSVSVQDDG 75 RGIPTGIHPE85 EGVSAAEVIM95 TVLGVGVSVV123 NALSQKLELV133 IQREGKIHRQ 143 IYEHGVPQAP153 LAVTGETEKT163 GTMVRFWPSL173 ETFTNVTEFE183 YEILAKRLRE 193 LSFLNSGVSI203 RLRDKRDGKE213 DHFHY
|
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .27K or .27K2 or .27K3 or :327K;style chemicals stick;color identity;select .A:43 or .A:46 or .A:47 or .A:50 or .A:71 or .A:73 or .A:78 or .A:79 or .A:94 or .A:95 or .A:120 or .A:165 or .A:166 or .A:167; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 4,4'-Thiodiphenol | Ligand Info | |||||
| Structure Description | Bacterial GyrB ATPase domain in complex with a chemical fragment | PDB:5Z4H | ||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [17] |
| PDB Sequence |
LDAVRKRPGM
25 YIGDTDDGTG35 LHHMVFEVVD45 NAIDEALAGH55 CKEIIVTIHA65 DNSVSVQDDG 75 RGIPTGIHPE85 EGVSAAEVIM95 TVLHGVGVSV122 VNALSQKLEL132 VIQREGKIHR 142 QIYEHGVPQA152 PLAVTGETEK162 TGTMVRFWPS172 LETFTNVTEF182 EYEILAKRLR 192 ELSFLNSGVS202 IRLRDKRDGK212 EDHFHY
|
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .A8K or .A8K2 or .A8K3 or :3A8K;style chemicals stick;color identity;select .A:43 or .A:46 or .A:47 or .A:50 or .A:71 or .A:72 or .A:73 or .A:78 or .A:91 or .A:92 or .A:94 or .A:95 or .A:120 or .A:132 or .A:134 or .A:165 or .A:166 or .A:167; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: (3,4-Dichlorophenyl)hydrazine | Ligand Info | |||||
| Structure Description | Bacterial GyrB ATPase domain in complex with (3,4-dichlorophenyl)hydrazine | PDB:5Z9B | ||||
| Method | X-ray diffraction | Resolution | 2.10 Å | Mutation | No | [17] |
| PDB Sequence |
LDAVRKRPGM
25 YIGDTDDGTG35 LHHMVFEVVD45 NAIDEALAGH55 CKEIIVTIHA65 DNSVSVQDDG 75 RGIPTGIHPE85 EGVSAAEVIM95 TVLHGVGVSV122 VNALSQKLEL132 VIQREGKIHR 142 QIYEHGVPQA152 PLAVTGETEK162 TGTMVRFWPS172 LETFTNVTEF182 EYEILAKRLR 192 ELSFLNSGVS202 IRLRDKRDGK212 EDHFHY
|
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .HX3 or .HX32 or .HX33 or :3HX3;style chemicals stick;color identity;select .A:43 or .A:46 or .A:47 or .A:50 or .A:71 or .A:72 or .A:73 or .A:78 or .A:94 or .A:95 or .A:120 or .A:165 or .A:166 or .A:167; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| Ligand Name: 4,6-Dichloro-2-(methylthio)pyrimidine | Ligand Info | |||||
| Structure Description | S.aureus GyrB ATPase domain in complex with 4,6-dichloro-2-(methylthio)pyrimidine | PDB:5Z9N | ||||
| Method | X-ray diffraction | Resolution | 2.54 Å | Mutation | No | [17] |
| PDB Sequence |
GLDAVRKRPG
24 MYIGDTDDGT34 GLHHMVFEVV44 DNAIDEALAG54 HCKEIIVTIH64 ADNSVSVQDD 74 GRGIPTGIHP84 EEGVSAAEVI94 MTVLHGVGVS121 VVNALSQKLE131 LVIQREGKIH 141 RQIYEHGVPQ151 APLAVTGETE161 KTGTMVRFWP171 SLETFTNVTE181 FEYEILAKRL 191 RELSFLNSGV201 SIRLRDKRDG211 KEDHFHYEG
|
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .HX5 or .HX52 or .HX53 or :3HX5;style chemicals stick;color identity;select .A:43 or .A:46 or .A:47 or .A:50 or .A:71 or .A:72 or .A:73 or .A:77 or .A:78 or .A:94 or .A:120 or .A:165 or .A:166 or .A:167; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: Benzofuran-2-carboxylic acid | Ligand Info | |||||
| Structure Description | Bacterial GyrB ATPase domain in complex with a chemical fragment | PDB:5Z9M | ||||
| Method | X-ray diffraction | Resolution | 2.74 Å | Mutation | No | [17] |
| PDB Sequence |
LDAVRKRPGM
25 YIGDTDDGTG35 LHHMVFEVVD45 NAIDEALAGH55 CKEIIVTIHA65 DNSVSVQDDG 75 RGIPTGIHPE85 EGVSAAEVIM95 TVLGVGVSVV123 NALSQKLELV133 IQREGKIHRQ 143 IYEHGVPQAP153 LAVTGETEKT163 GTMVRFWPSL173 ETFTNVTEFE183 YEILAKRLRE 193 LSFLNSGVSI203 RLRDKRDGKE213 DHFHYEG
|
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .BZ2 or .BZ22 or .BZ23 or :3BZ2;style chemicals stick;color identity;select .A:46 or .A:50 or .A:76 or .A:77 or .A:78 or .A:79 or .A:94 or .A:136; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: Methyl 3,4-dihydroxybenzoate | Ligand Info | |||||
| Structure Description | E. coli GyrB ATPase domain in complex with methyl 3,4-dihydroxybenzoate | PDB:7DPR | ||||
| Method | X-ray diffraction | Resolution | 1.75 Å | Mutation | No | [2] |
| PDB Sequence |
LDAVRKRPGM
25 YIGDTDDGTG35 LHHMVFEVVD45 NAIDEALAGH55 CKEIIVTIHA65 DNSVSVQDDG 75 RGIPTGIHPE85 EGVSAAEVIM95 TVLGVGVSVV123 NALSQKLELV133 IQREGKIHRQ 143 IYEHGVPQAP153 LAVTGETEKT163 GTMVRFWPSL173 ETFTNVTEFE183 YEILAKRLRE 193 LSFLNSGVSI203 RLRDKRDGKE213 DHFHY
|
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .HE9 or .HE92 or .HE93 or :3HE9;style chemicals stick;color identity;select .A:43 or .A:46 or .A:47 or .A:50 or .A:71 or .A:72 or .A:73 or .A:78 or .A:94 or .A:95 or .A:120 or .A:165 or .A:166 or .A:167; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: Methyl 2,4-dihydroxybenzoate | Ligand Info | |||||
| Structure Description | E. coli GyrB ATPase domain in complex with methyl 2,4-dihydroxybenzoate | PDB:7DQF | ||||
| Method | X-ray diffraction | Resolution | 1.80 Å | Mutation | No | [2] |
| PDB Sequence |
LDAVRKRPGM
25 YIGDTDDGTG35 LHHMVFEVVD45 NAIDEALAGH55 CKEIIVTIHA65 DNSVSVQDDG 75 RGIPTGIHPE85 EGVSAAEVIM95 TVLGVGVSVV123 NALSQKLELV133 IQREGKIHRQ 143 IYEHGVPQAP153 LAVTGETEKT163 GTMVRFWPSL173 ETFTNVTEFE183 YEILAKRLRE 193 LSFLNSGVSI203 RLRDKRDGKE213 DHFHY
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .HF9 or .HF92 or .HF93 or :3HF9;style chemicals stick;color identity;select .A:43 or .A:46 or .A:47 or .A:50 or .A:71 or .A:72 or .A:73 or .A:78 or .A:94 or .A:95 or .A:120 or .A:165 or .A:166 or .A:167; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 4-Chlorophenol | Ligand Info | |||||
| Structure Description | E. coli GyrB ATPase domain in complex with 4-chlorophenol | PDB:7DQW | ||||
| Method | X-ray diffraction | Resolution | 1.88 Å | Mutation | No | [2] |
| PDB Sequence |
LDAVRKRPGM
25 YIGDTDDGTG35 LHHMVFEVVD45 NAIDEALAGH55 CKEIIVTIHA65 DNSVSVQDDG 75 RGIPTGIHPE85 EGVSAAEVIM95 TVLGVGVSVV123 NALSQKLELV133 IQREGKIHRQ 143 IYEHGVPQAP153 LAVTGETEKT163 GTMVRFWPSL173 ETFTNVTEFE183 YEILAKRLRE 193 LSFLNSGVSI203 RLRDKRDGKE213 DHFHY
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .4CH or .4CH2 or .4CH3 or :34CH;style chemicals stick;color identity;select .A:43 or .A:46 or .A:47 or .A:50 or .A:71 or .A:72 or .A:73 or .A:78 or .A:94 or .A:95 or .A:120 or .A:165 or .A:166 or .A:167; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 4-Nitrophenol | Ligand Info | |||||
| Structure Description | E. coli GyrB ATPase domain in complex with 4-nitropheno | PDB:7DOR | ||||
| Method | X-ray diffraction | Resolution | 1.89 Å | Mutation | No | [2] |
| PDB Sequence |
LDAVRKRPGM
25 YIGDTDDGTG35 LHHMVFEVVD45 NAIDEALAGH55 CKEIIVTIHA65 DNSVSVQDDG 75 RGIPTGIHPE85 EGVSAAEVIM95 TVLGVGVSVV123 NALSQKLELV133 IQREGKIHRQ 143 IYEHGVPQAP153 LAVTGETEKT163 GTMVRFWPSL173 ETFTNVTEFE183 YEILAKRLRE 193 LSFLNSGVSI203 RLRDKRDGKE213 DHFHY
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .NPO or .NPO2 or .NPO3 or :3NPO;style chemicals stick;color identity;select .A:43 or .A:46 or .A:47 or .A:50 or .A:71 or .A:72 or .A:73 or .A:78 or .A:94 or .A:95 or .A:120 or .A:165 or .A:166 or .A:167; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 4-(4-bromanylpyrazol-1-yl)-6-(ethylcarbamoylamino)-~{N}-pyridin-3-yl-pyridine-3-carboxamide | Ligand Info | |||||
| Structure Description | Crystal Structure of E. coli GyraseB 24kDa in complex with 4-(4-bromo-1H-pyrazol-1-yl)-6-[(ethylcarbamoyl)amino]-N-(pyridin-3-yl)pyridine-3-carboxamide | PDB:6F86 | ||||
| Method | X-ray diffraction | Resolution | 1.90 Å | Mutation | No | [7] |
| PDB Sequence |
GLDAVRKRPG
24 MYIGDTDDGT34 GLHHMVFEVV44 DNAIDEALAG54 HCKEIIVTIH64 ADNSVSVQDD 74 GRGIPTGIHP84 EEGVSAAEVI94 MTVLGVGVSV122 VNALSQKLEL132 VIQREGKIHR 142 QIYEHGVPQA152 PLAVTGETEK162 TGTMVRFWPS172 LETFTNVTEF182 EYEILAKRLR 192 ELSFLNSGVS202 IRLRDKRDGK212 EDHFHYE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .CWW or .CWW2 or .CWW3 or :3CWW;style chemicals stick;color identity;select .A:43 or .A:46 or .A:47 or .A:50 or .A:71 or .A:72 or .A:73 or .A:76 or .A:77 or .A:78 or .A:79 or .A:94 or .A:136 or .A:165 or .A:166 or .A:167; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 3',4'-Dihydroxyacetophenone | Ligand Info | |||||
| Structure Description | E. coli GyrB ATPase domain in complex with 3,4-Dihydroxyacetophenone | PDB:7DQJ | ||||
| Method | X-ray diffraction | Resolution | 1.92 Å | Mutation | No | [2] |
| PDB Sequence |
LDAVRKRPGM
25 YIGDTDDGTG35 LHHMVFEVVD45 NAIDEALAGH55 CKEIIVTIHA65 DNSVSVQDDG 75 RGIPTGIHPE85 EGVSAAEVIM95 TVLGVGVSVV123 NALSQKLELV133 IQREGKIHRQ 143 IYEHGVPQAP153 LAVTGETEKT163 GTMVRFWPSL173 ETFTNVTEFE183 YEILAKRLRE 193 LSFLNSGVSI203 RLRDKRDGKE213 DHFHY
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .HFO or .HFO2 or .HFO3 or :3HFO;style chemicals stick;color identity;select .A:43 or .A:46 or .A:47 or .A:50 or .A:71 or .A:72 or .A:73 or .A:78 or .A:94 or .A:95 or .A:120 or .A:165 or .A:166 or .A:167; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 4-Chlorocatechol | Ligand Info | |||||
| Structure Description | E. coli GyrB ATPase domain in complex with 4-chlorobenzene-1,2-diol | PDB:7DQL | ||||
| Method | X-ray diffraction | Resolution | 1.93 Å | Mutation | No | [2] |
| PDB Sequence |
LDAVRKRPGM
25 YIGDTDDGTG35 LHHMVFEVVD45 NAIDEALAGH55 CKEIIVTIHA65 DNSVSVQDDG 75 RGIPTGIHPE85 EGVSAAEVIM95 TVLGVGVSVV123 NALSQKLELV133 IQREGKIHRQ 143 IYEHGVPQAP153 LAVTGETEKT163 GTMVRFWPSL173 ETFTNVTEFE183 YEILAKRLRE 193 LSFLNSGVSI203 RLRDKRDGKE213 DHFHY
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .4CL or .4CL2 or .4CL3 or :34CL;style chemicals stick;color identity;select .A:43 or .A:46 or .A:47 or .A:50 or .A:71 or .A:72 or .A:73 or .A:78 or .A:94 or .A:95 or .A:120 or .A:165 or .A:166 or .A:167; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: Methyl 4-hydroxycinnamate | Ligand Info | |||||
| Structure Description | E. coli GyrB ATPase domain in complex with Methyl 4-hydroxycinnamate | PDB:7DPS | ||||
| Method | X-ray diffraction | Resolution | 2.26 Å | Mutation | No | [2] |
| PDB Sequence |
LDAVRKRPGM
25 YIGDTDDGTG35 LHHMVFEVVD45 NAIDEALAGH55 CKEIIVTIHA65 DNSVSVQDDG 75 RGIPTGIHPE85 EGVSAAEVIM95 TVLGVGVSVV123 NALSQKLELV133 IQREGKIHRQ 143 IYEHGVPQAP153 LAVTGETEKT163 GTMVRFWPSL173 ETFTNVTEFE183 YEILAKRLRE 193 LSFLNSGVSI203 RLRDKRDGKE213 DHFHY
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .HF6 or .HF62 or .HF63 or :3HF6;style chemicals stick;color identity;select .A:43 or .A:46 or .A:47 or .A:50 or .A:71 or .A:73 or .A:78 or .A:79 or .A:94 or .A:120 or .A:165 or .A:167; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: (2Z)-2-[[4,5-bis(bromanyl)-1H-pyrrol-2-yl]carbonylimino]-3-(phenylmethyl)-1,3-benzothiazole-6-carboxylic acid | Ligand Info | |||||
| Structure Description | E.coli GyrB24 with inhibitor KOB20 (EBL2583) | PDB:7P2X | ||||
| Method | X-ray diffraction | Resolution | 1.60 Å | Mutation | No | [18] |
| PDB Sequence |
SSIKVLKGLD
17 AVRKRPGMYI27 GDTDDGTGLH37 HMVFEVVDNA47 IDEALAGHCK57 EIIVTIHADN 67 SVSVQDDGRG77 IPTGIHPEEG87 VSAAEVIMTV97 LHAGVGVSVV123 NALSQKLELV 133 IQREGKIHRQ143 IYEHGVPQAP153 LAVTGETEKT163 GTMVRFWPSL173 ETFTNVTEFE 183 YEILAKRLRE193 LSFLNSGVSI203 RLRDKRDGKE213 DHFHY
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .4Q6 or .4Q62 or .4Q63 or :34Q6;style chemicals stick;color identity;select .A:43 or .A:46 or .A:47 or .A:50 or .A:71 or .A:73 or .A:76 or .A:77 or .A:78 or .A:79 or .A:94 or .A:120 or .A:136 or .A:165 or .A:167; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | The entropic penalty of ordered water accounts for weaker binding of the antibiotic novobiocin to a resistant mutant of DNA gyrase: a thermodynamic and crystallographic study. Biochemistry. 1997 Aug 12;36(32):9663-73. | ||||
| REF 2 | Identification of new building blocks by fragment screening for discovering GyrB inhibitors. Bioorg Chem. 2021 Sep;114:105040. | ||||
| REF 3 | Structure of the N-terminal Gyrase B fragment in complex with ADP?Pi reveals rigid-body motion induced by ATP hydrolysis. PLoS One. 2014 Sep 9;9(9):e107289. | ||||
| REF 4 | The role of monovalent cations in the ATPase reaction of DNA gyrase. Acta Crystallogr D Biol Crystallogr. 2015 Apr;71(Pt 4):996-1005. | ||||
| REF 5 | DNA gyrase interaction with coumarin-based inhibitors: the role of the hydroxybenzoate isopentenyl moiety and the 5'-methyl group of the noviose. Biochemistry. 2002 Jun 11;41(23):7217-23. | ||||
| REF 6 | Discovery of Benzothiazole Scaffold-Based DNA Gyrase B Inhibitors. J Med Chem. 2016 Oct 13;59(19):8941-8954. | ||||
| REF 7 | New insights into the binding mode of pyridine-3-carboxamide inhibitors of E. coli DNA gyrase. Bioorg Med Chem. 2019 Aug 15;27(16):3546-3550. | ||||
| REF 8 | E.coli GyrB24 with inhibitor LSJ38 (EBL2684) | ||||
| REF 9 | E.coli GyrB24 with inhibitor LMD43 (EBL2560) | ||||
| REF 10 | Structure-based discovery of substituted 4,5'-bithiazoles as novel DNA gyrase inhibitors. J Med Chem. 2012 Jul 26;55(14):6413-26. | ||||
| REF 11 | Exploring the Chemical Space of Benzothiazole-Based DNA Gyrase B Inhibitors. ACS Med Chem Lett. 2020 Oct 15;11(12):2433-2440. | ||||
| REF 12 | E.coli GyrB24 with inhibitor LMD92 (EBL2682) | ||||
| REF 13 | Lead optimization of 8-(methylamino)-2-oxo-1,2-dihydroquinolines as bacterial type II topoisomerase inhibitors. Bioorg Med Chem. 2020 Nov 15;28(22):115776. | ||||
| REF 14 | Lead Identification of 8-(Methylamino)-2-oxo-1,2-dihydroquinoline Derivatives as DNA Gyrase Inhibitors: Hit-to-Lead Generation Involving Thermodynamic Evaluation. ACS Omega. 2020 Apr 24;5(17):10145-10159. | ||||
| REF 15 | The DNA Gyrase B ATP binding domain of Escherichia coli in complex with a small molecule inhibitor. | ||||
| REF 16 | Pyrrolopyrimidine inhibitors of DNA gyrase B (GyrB) and topoisomerase IV (ParE). Part I: Structure guided discovery and optimization of dual targeting agents with potent, broad-spectrum enzymatic activity. Bioorg Med Chem Lett. 2013 Mar 1;23(5):1529-36. | ||||
| REF 17 | Identification of an auxiliary druggable pocket in the DNA gyrase ATPase domain using fragment probes. Medchemcomm. 2018 Jul 4;9(10):1619-1629. | ||||
| REF 18 | E.coli GyrB24 with inhibitor KOB20 (EBL2583) | ||||
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