Binding Site Information of Target
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T83369 | Target Info | |||
| Target Name | Coagulation factor IX (F9) | ||||
| Synonyms | Plasma thromboplastin component; PTC protein; Factor IX; Christmas factor | ||||
| Target Type | Successful Target | ||||
| Gene Name | F9 | ||||
| Biochemical Class | Peptidase | ||||
| UniProt ID | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: 2-Methyl-2-Propanol | Ligand Info | |||||
| Structure Description | HUMAN COAGULATION FACTOR IXA IN COMPLEX WITH P-AMINO BENZAMIDINE | PDB:1RFN | ||||
| Method | X-ray diffraction | Resolution | 2.80 Å | Mutation | No | [1] |
| PDB Sequence |
VVGGEDAKPG
25 QFPWQVVLNG35 KVDAFCGGSI46 VNEKWIVTAA56 HCVETGVKIT65 VVAGEHNIEE 75 TEHTEQKRNV85 IRIIPHHNYN95 AAINKYNHDI103 ALLELDEPLV113 LNSYVTPICI 123 ADKEYTNIFL131 KFGSGYVSGW141 GRVFHKGRSA152 LVLQYLRVPL162 VDRATCLRST 172 KFTIYNNMFC182 AGFHEGGRDS190 CQGDSGGPHV200 TEVEGTSFLT210 GIISWGEECA 221 MKGKYGIYTK230 VSRYVNWIKE240 KTKLT
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| Ligand Name: UDP-glucose | Ligand Info | |||||
| Structure Description | Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese,acceptor ligand and UDP-Glucose | PDB:4WMA | ||||
| Method | X-ray diffraction | Resolution | 1.62 Å | Mutation | No | [2] |
| PDB Sequence |
QCESNPCLNG
59 GSCKDDINSY69 ECWCPFGFEG79 KNCEL
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| Ligand Name: Uridine-5'-Diphosphate | Ligand Info | |||||
| Structure Description | Crystal structure of Drosophila Poglut1 (Rumi) complexed with its substrate protein (EGF repeat) and UDP | PDB:5F85 | ||||
| Method | X-ray diffraction | Resolution | 2.15 Å | Mutation | No | [3] |
| PDB Sequence |
GDQCESNPCL
57 NGGSCKDDIN67 SYECWCPFGF77 EGKNCELLE
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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 .UDP or .UDP2 or .UDP3 or :3UDP;style chemicals stick;color identity;select .B:52; color #00ffc7; 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: Beta-D-Glucose | Ligand Info | |||||
| Structure Description | Crystal structure of Drosophila Poglut1 (Rumi) complexed with its glycoprotein product (glucosylated EGF repeat) and UDP | PDB:5F84 | ||||
| Method | X-ray diffraction | Resolution | 2.50 Å | Mutation | No | [3] |
| PDB Sequence |
GDQCESNPCL
57 NGGSCKDDIN67 SYECWCPFGF77 EGKNCELLE
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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 .BGC or .BGC2 or .BGC3 or :3BGC;style chemicals stick;color identity;select .B:52 or .B:53; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: P-Amino benzamidine | Ligand Info | |||||
| Structure Description | CRYSTAL STRUCTURE OF HUMAN COAGULATION FACTOR IXa | PDB:6MV4 | ||||
| Method | X-ray diffraction | Resolution | 1.37 Å | Mutation | No | [4] |
| PDB Sequence |
VVGGEDAKPG
25 QFPWQVVLNG35 KVDAFCGGSI46 VNEKWIVTAA56 HCVETGVKIT65 VVAGEHNIEE 75 TEHTEQKRNV85 IRIIPHHNYN95 AAINKYNHDI103 ALLELDEPLV113 LNSYVTPICI 123 ADKEYTNIFL131 KFGSGYVSGW141 GRVFHKGRSA152 LVLQYLRVPL162 VDRATCLRST 172 KFTIYNNMFC182 AGFHEGGRDS190 CQGDSGGPHV200 TEVEGTSFLT210 GIISWGEECA 221 MKGKYGIYTK230 VSRYVNWIKE240 KTKLT
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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 .PBZ or .PBZ2 or .PBZ3 or :3PBZ;style chemicals stick;color identity;select .H:57 or .H:189 or .H:190 or .H:191 or .H:192 or .H:193 or .H:195 or .H:213 or .H:214 or .H:215 or .H:216 or .H:217 or .H:219 or .H:220 or .H:221 or .H:225 or .H:226 or .H:227 or .H:228; color #00ffc7; 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: N-[(1s,4s,7r)-2-(3-Amino-4-Chloro[1,2]oxazolo[5,4-C]pyridin-7-Yl)-2-Azabicyclo[2.2.1]heptan-7-Yl]-2-Chloro-4-(3-Methyl-1h-1,2,4-Triazol-1-Yl)benzamide | Ligand Info | |||||
| Structure Description | Discovery of novel aminobenzisoxazole derivatives as orally available factor IXa inhibitors | PDB:5TNT | ||||
| Method | X-ray diffraction | Resolution | 1.40 Å | Mutation | Yes | [5] |
| PDB Sequence |
VVGGEDAKPG
25 QFPWQVVLNG35 KVDAFCGGSI46 VNEKWIVTAA56 HCVETGVKIT65 VVAGEHNIEE 75 TEHTEQKRNV85 IRIIPHHNYN95 AAINKYNHDI103 ALLELDEPLV113 LNSYVTPICI 123 ADKEYTNIFL131 KFGSGYVSGW141 GRVFHKGASA152 LVLQYLRVPL162 VDRATCLRST 172 KFTIYNNMFC182 AGFHEGGRDS190 CQGDSGGPHV200 TEVEGTSFLT210 GIISWGEECA 221 MKGKYGIYTK230 VSRYVNWIKE240 KTKLT
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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 .7GQ or .7GQ2 or .7GQ3 or :37GQ;style chemicals stick;color identity;select .A:57 or .A:97 or .A:98 or .A:99 or .A:143 or .A:147 or .A:148 or .A:174 or .A:175 or .A:189 or .A:190 or .A:191 or .A:192 or .A:193 or .A:194 or .A:195 or .A:213 or .A:214 or .A:215 or .A:216 or .A:217 or .A:219 or .A:220 or .A:221 or .A:225 or .A:226 or .A:227 or .A:228; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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HIS57
4.880
ASN97
4.155
LYS98
4.592
TYR99
2.585
ARG143
4.099
HIS147
2.149
LYS148
4.456
PHE174
2.510
THR175
4.122
ASP189
2.439
SER190
2.009
CYS191
2.885
GLN192
2.417
GLY193
3.853
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| Ligand Name: N-[(2r)-10-Hydroxy-2,7-Dimethyl-1,2,3,4-Tetrahydropyrido[1,2-B]indazol-2-Yl]-4-(4h-1,2,4-Triazol-4-Yl)benzamide | Ligand Info | |||||
| Structure Description | Rapid development of two Factor IXa inhibitors from Hit to Lead | PDB:4Z0K | ||||
| Method | X-ray diffraction | Resolution | 1.41 Å | Mutation | Yes | [6] |
| PDB Sequence |
VVGGEDAKPG
25 QFPWQVVLNG35 KVDAFCGGSI46 VNEKWIVTAA56 HCVETGVKIT65 VVAGEHNIEE 75 TEHTEQKRNV85 IRIIPHHNYN95 AAINKYNHDI103 ALLELDEPLV113 LNSYVTPICI 123 ADKEYTNIFL131 KFGSGYVSGW141 GRVFHKGASA152 LVLQYLRVPL162 VDRATCLRST 172 KFTIYNNMFC182 AGFHEGGRDS190 CQGDSGGPHV200 TEVEGTSFLT210 GIISWGEECA 221 MKGKYGIYTK230 VSRYVNWIKE240 KTKL
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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 .4LN or .4LN2 or .4LN3 or :34LN;style chemicals stick;color identity;select .A:97 or .A:99 or .A:147 or .A:174 or .A:189 or .A:190 or .A:191 or .A:192 or .A:193 or .A:194 or .A:195 or .A:213 or .A:214 or .A:215 or .A:216 or .A:217 or .A:219 or .A:220 or .A:221 or .A:226 or .A:227; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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ASN97
4.162
TYR99
2.829
HIS147
2.904
PHE174
3.240
ASP189
4.311
SER190
3.238
CYS191
2.970
GLN192
2.741
GLY193
4.630
ASP194
3.832
SER195
3.037
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| Ligand Name: N-[2-(5,6-Dimethyl-1h-Benzimidazol-2-Yl)ethyl]-4-(4h-1,2,4-Triazol-4-Yl)benzamide | Ligand Info | |||||
| Structure Description | Rapid development of two Factor IXa inhibitors from Hit to Lead | PDB:4YZU | ||||
| Method | X-ray diffraction | Resolution | 1.41 Å | Mutation | Yes | [6] |
| PDB Sequence |
VVGGEDAKPG
25 QFPWQVVLNG35 KVDAFCGGSI46 VNEKWIVTAA56 HCVETGVKIT65 VVAGEHNIEE 75 TEHTEQKRNV85 IRIIPHHNYN95 AAINKYNHDI103 ALLELDEPLV113 LNSYVTPICI 123 ADKEYTNIFL131 KFGSGYVSGW141 GRVFHKGASA152 LVLQYLRVPL162 VDRATCLRST 172 KFTIYNNMFC182 AGFHEGGRDS190 CQGDSGGPHV200 TEVEGTSFLT210 GIISWGEECA 221 MKGKYGIYTK230 VSRYVNWIKE240 KTKLT
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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 .4K6 or .4K62 or .4K63 or :34K6;style chemicals stick;color identity;select .A:97 or .A:99 or .A:147 or .A:174 or .A:175 or .A:189 or .A:190 or .A:191 or .A:192 or .A:193 or .A:194 or .A:195 or .A:213 or .A:214 or .A:215 or .A:216 or .A:217 or .A:219 or .A:220 or .A:226 or .A:227; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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ASN97
4.276
TYR99
2.966
HIS147
4.661
PHE174
2.965
THR175
4.730
ASP189
4.094
SER190
3.300
CYS191
2.903
GLN192
2.940
GLY193
4.650
ASP194
3.900
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| Ligand Name: L-Alpha-Glutamyl-N-{(1s)-4-{[amino(Iminio)methyl]amino}-1-[(1s)-2-Chloro-1-Hydroxyethyl]butyl}glycinamide | Ligand Info | |||||
| Structure Description | Crystal structure of factor IXa variant K98T in complex with EGR-chloromethylketone | PDB:5JB8 | ||||
| Method | X-ray diffraction | Resolution | 1.45 Å | Mutation | Yes | [7] |
| PDB Sequence |
VVGGEDAKPG
25 QFPWQVVLNG35 KVDAFCGGSI46 VNEKWIVTAA56 HCVETGVKIT65 VVAGEHNIEE 75 TEHTEQKRNV85 IRIIPHHNYN95 AAINTYNHDI103 ALLELDEPLV113 LNSYVTPICI 123 ADKEYTNIFL131 KFGSGYVSGW141 GRVFHKGRSA152 LVLQYLRVPL162 VDRATCLRST 172 KFTIYNNMFC182 AGFHEGGRDS190 CQGDSGGPHV200 TEVEGTSFLT210 GIISWGEECA 221 MKGKYGIYTK230 VSRYVNWIKE240 KTKLT
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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 .0GJ or .0GJ2 or .0GJ3 or :30GJ;style chemicals stick;color identity;select .S:41 or .S:42 or .S:57 or .S:58 or .S:99 or .S:143 or .S:147 or .S:174 or .S:189 or .S:190 or .S:191 or .S:192 or .S:193 or .S:194 or .S:195 or .S:213 or .S:214 or .S:215 or .S:216 or .S:217 or .S:219 or .S:220 or .S:221 or .S:225 or .S:226 or .S:227 or .S:228; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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PHE41
3.873
CYS42
3.418
HIS57
1.463
CYS58
3.763
TYR99
2.470
ARG143
4.713
HIS147
3.693
PHE174
4.260
ASP189
2.034
SER190
2.383
CYS191
2.901
GLN192
2.256
GLY193
2.466
ASP194
3.635
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 2-Chloranyl-~{n}-[(7~{s})-2-Methyl-7-Phenyl-10-(1~{h}-1,2,3,4-Tetrazol-5-Yl)-8,9-Dihydro-6~{h}-Pyrido[1,2-A]indol-7-Yl]-4-(1,2,4-Triazol-4-Yl)benzamide | Ligand Info | |||||
| Structure Description | Development of a novel tricyclic class of potent and selective FIXa inhibitors | PDB:5EGM | ||||
| Method | X-ray diffraction | Resolution | 1.84 Å | Mutation | Yes | [8] |
| PDB Sequence |
VVGGEDAKPG
25 QFPWQVVLNG35 KVDAFCGGSI46 VNEKWIVTAA56 HCVETGVKIT65 VVAGEHNIEE 75 TEHTEQKRNV85 IRIIPHHNYN95 AAINKYNHDI103 ALLELDEPLV113 LNSYVTPICI 123 ADKEYTNIFL131 KFGSGYVSGW141 GRVFHKGASA152 LVLQYLRVPL162 VDRATCLRST 172 KFTIYNNMFC182 AGFHEGGRDS190 CQGDSGGPHV200 TEVEGTSFLT210 GIISWGEECA 221 MKGKYGIYTK230 VSRYVNWIKE240 KTKLT
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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 .5NY or .5NY2 or .5NY3 or :35NY;style chemicals stick;color identity;select .A:57 or .A:97 or .A:98 or .A:99 or .A:143 or .A:147 or .A:148 or .A:174 or .A:190 or .A:191 or .A:192 or .A:193 or .A:194 or .A:195 or .A:213 or .A:214 or .A:215 or .A:216 or .A:217 or .A:219 or .A:220 or .A:226 or .A:227; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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HIS57
2.899
ASN97
3.867
LYS98
3.663
TYR99
2.903
ARG143
4.906
HIS147
3.015
LYS148
2.873
PHE174
2.687
SER190
2.409
CYS191
2.455
GLN192
2.740
GLY193
3.890
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| Ligand Name: 2,6-Dichloro-N-[(2r)-2-(5,6-Dimethyl-1h-Benzimidazol-2-Yl)-2-Phenylethyl]-4-(4h-1,2,4-Triazol-4-Yl)benzamide | Ligand Info | |||||
| Structure Description | Development of a novel class of potent and selective FIXa inhibitors | PDB:4ZAE | ||||
| Method | X-ray diffraction | Resolution | 1.86 Å | Mutation | Yes | [9] |
| PDB Sequence |
VVGGEDAKPG
25 QFPWQVVLNG35 KVDAFCGGSI46 VNEKWIVTAA56 HCVETGVKIT65 VVAGEHNIEE 75 TEHTEQKRNV85 IRIIPHHNYN95 AAINKYNHDI103 ALLELDEPLV113 LNSYVTPICI 123 ADKEYTNIFL131 KFGSGYVSGW141 GRVFHKGASA152 LVLQYLRVPL162 VDRATCLRST 172 KFTIYNNMFC182 AGFHEGGRDS190 CQGDSGGPHV200 TEVEGTSFLT210 GIISWGEECA 221 MKGKYGIYTK230 VSRYVNWIKE240 KTKL
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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 .4M1 or .4M12 or .4M13 or :34M1;style chemicals stick;color identity;select .A:97 or .A:99 or .A:143 or .A:145 or .A:147 or .A:148 or .A:149 or .A:174 or .A:175 or .A:189 or .A:190 or .A:191 or .A:192 or .A:193 or .A:194 or .A:195 or .A:213 or .A:214 or .A:215 or .A:216 or .A:217 or .A:219 or .A:220 or .A:221 or .A:225 or .A:226 or .A:227 or .A:228; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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ASN97
4.453
TYR99
2.855
ARG143
2.727
PHE145
4.966
HIS147
2.511
LYS148
2.196
GLY149
4.752
PHE174
2.705
THR175
4.868
ASP189
3.009
SER190
2.225
CYS191
2.868
GLN192
2.759
GLY193
4.257
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| Ligand Name: 1-[5-(3,4-Dimethoxyphenyl)-1-benzothiophen-2-yl]methanediamine | Ligand Info | |||||
| Structure Description | Benzothiophene Inhibitors of Factor IXa | PDB:3LC3 | ||||
| Method | X-ray diffraction | Resolution | 1.90 Å | Mutation | No | [10] |
| PDB Sequence |
VVGGEDAKPG
25 QFPWQVVLNG35 KVDAFCGGSI46 VNEKWIVTAA56 HCVETGVKIT65 VVAGEHNIEE 75 TEHTEQKRNV85 IRIIPHHNYN95 AAINKYNHDI103 ALLELDEPLV113 LNSYVTPICI 123 ADKEYTNIFL131 KFGSGYVSGW141 GRVFHKGRSA152 LVLQYLRVPL162 VDRATCLRST 172 KFTIYNNMFC182 AGFHEGGRDS190 CQGDSGGPHV200 TEVEGTSFLT210 GIISWGEECA 221 MKGKYGIYTK230 VSRYVNWIKE240 KTKLT
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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 .IYX or .IYX2 or .IYX3 or :3IYX;style chemicals stick;color identity;select .A:57 or .A:97 or .A:98 or .A:99 or .A:147 or .A:174 or .A:189 or .A:190 or .A:191 or .A:192 or .A:193 or .A:195 or .A:213 or .A:214 or .A:215 or .A:216 or .A:217 or .A:219 or .A:220 or .A:221 or .A:225 or .A:226 or .A:227; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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HIS57
3.985
ASN97
3.476
LYS98
3.008
TYR99
3.074
HIS147
3.485
PHE174
3.452
ASP189
2.884
SER190
2.833
CYS191
3.660
GLN192
3.233
GLY193
4.868
SER195
3.034
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| Ligand Name: 3-Chloro-4-{[5-hydroxy-6-(4-methylphenyl)pyrimidin-4-yl]amino}benzene-1-carboximidamide | Ligand Info | |||||
| Structure Description | Discovery of Hydroxy Pyrimidine Factor IXa Inhibitors | PDB:6X5P | ||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | Yes | [11] |
| PDB Sequence |
VVGGEDAKPG
25 QFPWQVVLNG35 KVDAFCGGSI45 VNEKWIVTAA55 HCVEVKITVV67 AGEHNIEETE 77 HTEQKRNVIR87 IIPHHNYNAA97 INKYNHDIAL107 LELDEPLVLN117 SYVTPICIAD 127 KEYTNIFLKF137 GSGYVSGWGR147 VFHKGASALV157 LQYLRVPLVD167 RATCLRSTKF 177 TIYNNMFCAG187 FHEGGRDSCQ197 GDSGGPHVTE207 VEGTSFLTGI217 ISWGEECAMK 227 GKYGIYTKVS237 RYVNWIKEKT247 KL
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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 .UQD or .UQD2 or .UQD3 or :3UQD;style chemicals stick;color identity;select .A:40 or .A:41 or .A:56 or .A:57 or .A:58 or .A:59 or .A:100 or .A:101 or .A:194 or .A:195 or .A:196 or .A:197 or .A:198 or .A:199 or .A:200 or .A:218 or .A:219 or .A:220 or .A:221 or .A:222 or .A:223 or .A:224 or .A:225 or .A:226 or .A:229 or .A:230 or .A:231 or .A:232; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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PHE40
2.312
CYS41
2.943
HIS56
1.645
CYS57
2.368
VAL58
4.417
GLU59
3.376
LYS100
2.449
TYR101
3.547
ASP194
2.226
SER195
2.054
CYS196
2.959
GLN197
2.890
GLY198
2.969
ASP199
3.953
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| Ligand Name: 2-(4-Hydroxy-5-phenyl-1H-pyrazol-3-YL)-1H-benzoimidazole-5-carboxamidine | Ligand Info | |||||
| Structure Description | Discovery of Hydroxy Pyrimidine Factor IXa Inhibitors | PDB:6X5J | ||||
| Method | X-ray diffraction | Resolution | 2.51 Å | Mutation | No | [11] |
| PDB Sequence |
VVGGEDAKPG
25 QFPWQVVLNG35 KVDAFCGGSI45 VNEKWIVTAA55 HCVETGVKIT65 VVAGEHNIEE 75 TEHTEQKRNV85 IRIIPHHNYN95 AAINKYNHDI105 ALLELDEPLV115 LNSYVTPICI 125 ADKEYTNIFL135 KFGSGYVSGW145 GRVFHKGRSA155 LVLQYLRVPL165 VDRATCLRST 175 KFTIYNNMFC185 AGFHEGGRDS195 CQGDSGGPHV205 TEVEGTSFLT215 GIISWGEECA 225 MKGKYGIYTK235 VSRYVNWIKE245 KTKL
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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 .6NH or .6NH2 or .6NH3 or :36NH;style chemicals stick;color identity;select .A:40 or .A:41 or .A:56 or .A:57 or .A:100 or .A:101 or .A:194 or .A:195 or .A:196 or .A:197 or .A:198 or .A:199 or .A:200 or .A:218 or .A:219 or .A:220 or .A:221 or .A:222 or .A:223 or .A:224 or .A:225 or .A:229 or .A:230 or .A:231 or .A:232 or .A:233; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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PHE40
1.990
CYS41
3.144
HIS56
1.725
CYS57
2.595
LYS100
2.645
TYR101
3.383
ASP194
2.171
SER195
2.393
CYS196
2.955
GLN197
2.638
GLY198
3.871
ASP199
3.976
SER200
1.595
|
|||||
| Ligand Name: 1-{4-[(R)-phenyl(3-phenyl-1,2,4-oxadiazol-5-yl)methoxy]-1-benzothiophen-2-yl}methanediamine | Ligand Info | |||||
| Structure Description | Selective Benzothiophine Inhibitors of Factor IXa | PDB:3LC5 | ||||
| Method | X-ray diffraction | Resolution | 2.62 Å | Mutation | No | [12] |
| PDB Sequence |
VVGGEDAKPG
25 QFPWQVVLNG35 KVDAFCGGSI46 VNEKWIVTAA56 HCVETGVKIT65 VVAGEHNIEE 75 TEHTEQKRNV85 IRIIPHHNYN95 AAINKYNHDI103 ALLELDEPLV113 LNSYVTPICI 123 ADKEYTNIFL131 KFGSGYVSGW141 GRVFHKGRSA152 LVLQYLRVPL162 VDRATCLRST 172 KFTIYNNMFC182 AGFHEGGRDS190 CQGDSGGPHV200 TEVEGTSFLT210 GIISWGEECA 221 MKGKYGIYTK230 VSRYVNWIKE240 KTKLT
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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 .IZX or .IZX2 or .IZX3 or :3IZX;style chemicals stick;color identity;select .A:57 or .A:98 or .A:99 or .A:143 or .A:147 or .A:174 or .A:189 or .A:190 or .A:191 or .A:192 or .A:193 or .A:195 or .A:213 or .A:214 or .A:215 or .A:216 or .A:217 or .A:219 or .A:220 or .A:221 or .A:225 or .A:226 or .A:227 or .A:228; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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HIS57
4.926
LYS98
4.346
TYR99
4.279
ARG143
3.227
HIS147
3.625
PHE174
3.346
ASP189
2.703
SER190
2.635
CYS191
3.783
GLN192
3.269
GLY193
4.618
SER195
2.919
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| Ligand Name: 4-{[5-Hydroxy-6-(4-methylphenyl)pyrimidin-4-yl]amino}benzene-1-carboximidamide | Ligand Info | |||||
| Structure Description | Discovery of Hydroxy Pyrimidine Factor IXa Inhibitors | PDB:6X5L | ||||
| Method | X-ray diffraction | Resolution | 2.25 Å | Mutation | No | [11] |
| PDB Sequence |
VVGGEDAKPG
25 QFPWQVVLNG35 KVDAFCGGSI45 VNEKWIVTAA55 HCVEGVKITV66 VAGEHNIEET 76 EHTEQKRNVI86 RIIPHHNYNA96 AINKYNHDIA106 LLELDEPLVL116 NSYVTPICIA 126 DKEYTNIFLK136 FGSGYVSGWG146 RVFHKGRSAL156 VLQYLRVPLV166 DRATCLRSTK 176 FTIYNNMFCA186 GFHEGGRDSC196 QGDSGGPHVT206 EVEGTSFLTG216 IISWGEECAM 226 KGKYGIYTKV236 SRYVNWIKEK246 TKL
|
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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 .UQG or .UQG2 or .UQG3 or :3UQG;style chemicals stick;color identity;select .A:40 or .A:41 or .A:56 or .A:57 or .A:58 or .A:59 or .A:100 or .A:101 or .A:194 or .A:195 or .A:196 or .A:197 or .A:198 or .A:199 or .A:200 or .A:218 or .A:219 or .A:220 or .A:221 or .A:222 or .A:223 or .A:224 or .A:225 or .A:230 or .A:231 or .A:232 or .A:233; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
PHE40
2.234
CYS41
3.093
HIS56
1.835
CYS57
2.340
VAL58
4.395
GLU59
4.505
LYS100
2.192
TYR101
3.488
ASP194
2.127
SER195
2.453
CYS196
2.898
GLN197
2.671
GLY198
3.757
ASP199
3.947
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Coagulation factor IXa: the relaxed conformation of Tyr99 blocks substrate binding. Structure. 1999 Aug 15;7(8):989-96. | ||||
| REF 2 | Notch-modifying xylosyltransferase structures support an SNi-like retaining mechanism. Nat Chem Biol. 2015 Nov;11(11):847-54. | ||||
| REF 3 | Structural analysis of Notch-regulating Rumi reveals basis for pathogenic mutations. Nat Chem Biol. 2016 Sep;12(9):735-40. | ||||
| REF 4 | Sodium-site in serine protease domain of human coagulation factor IXa: evidence from the crystal structure and molecular dynamics simulations study. J Thromb Haemost. 2019 Apr;17(4):574-584. | ||||
| REF 5 | Discovery of novel aminobenzisoxazole derivatives as orally available factor IXa inhibitors. Bioorg Med Chem Lett. 2017 Jun 1;27(11):2622-2628. | ||||
| REF 6 | Rapid development of two factor IXa inhibitors from hit to lead. Bioorg Med Chem Lett. 2015 Jun 1;25(11):2321-5. | ||||
| REF 7 | Releasing the brakes in coagulation Factor IXa by co-operative maturation of the substrate-binding site. Biochem J. 2016 Aug 1;473(15):2395-411. | ||||
| REF 8 | Development of a novel tricyclic class of potent and selective FIXa inhibitors. Bioorg Med Chem Lett. 2015 Nov 15;25(22):5437-43. | ||||
| REF 9 | Development of a novel class of potent and selective FIXa inhibitors. Bioorg Med Chem Lett. 2015 Nov 1;25(21):4945-4949. | ||||
| REF 10 | Studies of benzothiophene template as potent factor IXa (FIXa) inhibitors in thrombosis. J Med Chem. 2010 Feb 25;53(4):1465-72. | ||||
| REF 11 | Discovery of hydroxy pyrimidine Factor IXa inhibitors. Bioorg Med Chem Lett. 2020 Aug 1;30(15):127279. | ||||
| REF 12 | Structure based drug design: development of potent and selective factor IXa (FIXa) inhibitors. J Med Chem. 2010 Feb 25;53(4):1473-82. | ||||
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