Target Binding Site Detail
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T76522 | Target Info | |||
| Target Name | Pyridoxal kinase (PDXK) | ||||
| Synonyms | Pyridoxine kinase; PDXK | ||||
| Target Type | Literature-reported Target | ||||
| Gene Name | PDXK | ||||
| Biochemical Class | Kinase | ||||
| UniProt ID | |||||
| Ligand General Information | Top | ||||
|---|---|---|---|---|---|
| Ligand Name | Adenosine triphosphate | Ligand Info | |||
| Canonical SMILES | C1=NC(=C2C(=N1)N(C=N2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N | ||||
| InChI | 1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1 | ||||
| InChIKey | ZKHQWZAMYRWXGA-KQYNXXCUSA-N | ||||
| PubChem Compound ID | 5957 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 3KEU Crystal Structure of Human PL Kinase with bound PLP and ATP | ||||||
| Method | X-ray diffraction | Resolution | 2.10 Å | Mutation | No | [1] |
| PDB Sequence |
EECRVLSIQS
12 HVIRGYVGNR22 AATFPLQVLG32 FEIDAVNSVQ42 FSNHTGYAHW52 KGQVLNSDEL 62 QELYEGLRLN72 NMNKYDYVLT82 GYTRDKSFLA92 MVVDIVQELK102 QQNPRLVYVC 112 DPVLGDKWDG122 EGSMYVPEDL132 LPVYKEKVVP142 LADIITPNQF152 EAELLSGRKI 162 HSQEEALRVM172 DMLHSMGPDT182 VVITSSDLPS192 PQGSNYLIVL202 GSQRRSVVME 217 RIRMDIRKVD227 AVFVGTGDLF237 AAMLLAWTHK247 HPNNLKVACE257 KTVSTLHHVL 267 QRTIQCAKAQ277 AGEGVRPSPM287 QLELRMVQSK297 RDIEDPEIVV307 QATVL |
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|
|
ASP113
3.097
VAL115
3.895
GLY117
4.429
ASP118
3.032
TYR127
3.771
THR148
3.917
PRO149
4.709
ASN150
3.284
GLU153
2.652
THR186
2.493
SER187
2.472
LEU199
3.941
VAL201
3.674
|
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| PDB ID: 4EN4 Crystal Structure of the Ternary Human PL Kinase-Ginkgotoxin-MgATP Complex | ||||||
| Method | X-ray diffraction | Resolution | 2.15 Å | Mutation | No | [2] |
| PDB Sequence |
EECRVLSIQS
12 HVIRGYVGNR22 AATFPLQVLG32 FEIDAVNSVQ42 FSNHTGYAHW52 KGQVLNSDEL 62 QELYEGLRLN72 NMNKYDYVLT82 GYTRDKSFLA92 MVVDIVQELK102 QQNPRLVYVC 112 DPVLGDKWDG122 EGSMYVPEDL132 LPVYKEKVVP142 LADIITPNQF152 EAELLSGRKI 162 HSQEEALRVM172 DMLHSMGPDT182 VVITSSDLPS192 PQGSNYLIVL202 GSQRRRNPAG 212 SVVMERIRMD222 IRKVDAVFVG232 TGDLFAAMLL242 AWTHKHPNNL252 KVACEKTVST 262 LHHVLQRTIQ272 CAKAQAGEGV282 RPSPMQLELR292 MVQSKRDIED302 PEIVVQATVL 312
|
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|
|
ASP113
2.998
VAL115
4.101
GLY117
4.870
ASP118
3.318
TYR127
3.858
THR148
4.664
PRO149
4.902
ASN150
3.381
GLU153
2.793
THR186
2.404
SER187
2.640
LEU199
4.001
VAL201
3.644
|
|||||
| PDB ID: 2YXU Human Pyridoxal Kinase | ||||||
| Method | X-ray diffraction | Resolution | 2.20 Å | Mutation | No | [3] |
| PDB Sequence |
EECRVLSIQS
12 HVIRGYVGNR22 AATFPLQVLG32 FEIDAVNSVQ42 FSNHTGYAHW52 KGQVLNSDEL 62 QELYEGLRLN72 NMNKYDYVLT82 GYTRDKSFLA92 MVVDIVQELK102 QQNPRLVYVC 112 DPVLGDKWDG122 EGSMYVPEDL132 LPVYKEKVVP142 LADIITPNQF152 EAELLSGRKI 162 HSQEEALRVM172 DMLHSMGPDT182 VVITSSDLPS192 PQGSNYLIVL202 GSQRRGSVVM 216 ERIRMDIRKV226 DAVFVGTGDL236 FAAMLLAWTH246 KHPNNLKVAC256 EKTVSTLHHV 266 LQRTIQCAKA276 QAGEGVRPSP286 MQLELRMVQS296 KRDIEDPEIV306 VQATVL |
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|
|
ASP113
2.985
PRO114
4.940
VAL115
3.925
GLY117
4.581
ASP118
2.846
TYR127
3.565
THR148
3.844
PRO149
4.542
ASN150
3.310
GLU153
2.553
THR186
2.536
SER187
2.541
LEU199
3.971
VAL201
3.553
|
|||||
| PDB ID: 3FHY Crystal structure of D235N mutant of human pyridoxal kinase | ||||||
| Method | X-ray diffraction | Resolution | 2.30 Å | Mutation | Yes | [4] |
| PDB Sequence |
ECRVLSIQSH
13 VIRGYVGNRA23 ATFPLQVLGF33 EIDAVNSVQF43 SNHTGYAHWK53 GQVLNSDELQ 63 ELYEGLRLNN73 MNKYDYVLTG83 YTRDKSFLAM93 VVDIVQELKQ103 QNPRLVYVCD 113 PVLGDKWDGE123 GSMYVPEDLL133 PVYKEKVVPL143 ADIITPNQFE153 AELLSGRKIH 163 SQEEALRVMD173 MLHSMGPDTV183 VITSSDLPSP193 QGSNYLIVLG203 SQRRRNPVVM 216 ERIRMDIRKV226 DAVFVGTGNL236 FAAMLLAWTH246 KHPNNLKVAC256 EKTVSTLHHV 266 LQRTIQCAKA276 QAGEGVRPSP286 MQLELRMVQS296 KRDIEDPEIV306 VQATVL |
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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 .ATP or .ATP2 or .ATP3 or :3ATP;style chemicals stick;color identity;select .A:113 or .A:115 or .A:117 or .A:118 or .A:127 or .A:148 or .A:150 or .A:153 or .A:186 or .A:187 or .A:199 or .A:201 or .A:223 or .A:224 or .A:225 or .A:226 or .A:228 or .A:230 or .A:233 or .A:234 or .A:235 or .A:237 or .A:260 or .A:263 or .A:267; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ASP113
2.954
VAL115
4.026
GLY117
4.205
ASP118
2.980
TYR127
3.975
THR148
4.873
ASN150
3.149
GLU153
2.812
THR186
2.372
SER187
2.299
LEU199
4.103
VAL201
3.621
ILE223
4.078
|
|||||
| PDB ID: 3FHX Crystal structure of D235A mutant of human pyridoxal kinase | ||||||
| Method | X-ray diffraction | Resolution | 2.50 Å | Mutation | Yes | [4] |
| PDB Sequence |
EECRVLSIQS
12 HVIRGYVGNR22 AATFPLQVLG32 FEIDAVNSVQ42 FSNHTGYAHW52 KGQVLNSDEL 62 QELYEGLRLN72 NMNKYDYVLT82 GYTRDKSFLA92 MVVDIVQELK102 QQNPRLVYVC 112 DPVLGDKWDG122 EGSMYVPEDL132 LPVYKEKVVP142 LADIITPNQF152 EAELLSGRKI 162 HSQEEALRVM172 DMLHSMGPDT182 VVITSSDLPS192 PQGSNYLIVL202 GSQRRRNPSV 214 VMERIRMDIR224 KVDAVFVGTG234 ALFAAMLLAW244 THKHPNNLKV254 ACEKTVSTLH 264 HVLQRTIQCA274 KAQAGEGVRP284 SPMQLELRMV294 QSKRDIEDPE304 IVVQATVL |
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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 .ATP or .ATP2 or .ATP3 or :3ATP;style chemicals stick;color identity;select .A:113 or .A:115 or .A:117 or .A:118 or .A:127 or .A:148 or .A:149 or .A:150 or .A:153 or .A:186 or .A:187 or .A:199 or .A:201 or .A:223 or .A:224 or .A:225 or .A:226 or .A:228 or .A:230 or .A:233 or .A:234 or .A:235 or .A:237 or .A:260 or .A:263 or .A:267; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ASP113
3.151
VAL115
4.088
GLY117
4.645
ASP118
2.891
TYR127
3.407
THR148
4.799
PRO149
4.987
ASN150
3.183
GLU153
2.534
THR186
2.442
SER187
2.461
LEU199
4.198
VAL201
3.755
|
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Crystal structure of PL kinase in complex with MgATP and PLP: Structural basis of severe induced MgATP substrate inhibition of the enzyme | ||||
| REF 2 | Crystal structures of human pyridoxal kinase in complex with the neurotoxins, ginkgotoxin and theophylline: insights into pyridoxal kinase inhibition. PLoS One. 2012;7(7):e40954. | ||||
| REF 3 | Crystal Structure of human pyridoxal kinase: structural basis of M(+) and M(2+) activation. Protein Sci. 2007 Oct;16(10):2184-94. | ||||
| REF 4 | Kinetic and structural studies of the role of the active site residue Asp235 of human pyridoxal kinase. Biochem Biophys Res Commun. 2009 Mar 27;381(1):12-5. | ||||
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