Binding Site Information of Target
| 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 | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: Adenosine triphosphate | Ligand Info | |||||
| Structure Description | Crystal Structure of Human PL Kinase with bound PLP and ATP | PDB:3KEU | ||||
| 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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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: Pyridoxal phosphate | Ligand Info | |||||
| Structure Description | Crystal Structure of Human PL Kinase with bound PLP and ATP | PDB:3KEU | ||||
| 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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| Ligand Name: PMID28870136-Compound-48 | Ligand Info | |||||
| Structure Description | Crystal Structure of Human PL Kinase with bound Theophylline | PDB:4EOH | ||||
| Method | X-ray diffraction | Resolution | 2.10 Å | Mutation | No | [2] |
| 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 SQRRVVMERI 219 RMDIRKVDAV229 FVGTGDLFAA239 MLLAWTHKHP249 NNLKVACEKT259 VSTLHHVLQR 269 TIQCAKAQAG279 EGVRPSPMQL289 ELRMVQSKRD299 IEDPEIVVQA309 TVL |
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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 .TEP or .TEP2 or .TEP3 or :3TEP;style chemicals stick;color identity;select .A:11 or .A:12 or .A:19 or .A:20 or .A:46 or .A:47 or .A:84 or .A:231 or .A:232 or .A:235; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: AMP-PNP | Ligand Info | |||||
| Structure Description | Crystal structure of a human pyridoxal kinase | PDB:2AJP | ||||
| Method | X-ray diffraction | Resolution | 2.50 Å | Mutation | No | [3] |
| PDB Sequence |
SRVLSIQSHV
14 IRGYVGNRAA24 TFPLQVLGFE34 IDAVNSVQFS44 NHTGYAHWKG54 QVLNSDELQE 64 LYEGLRLNNM74 NKYDYVLTGY84 TRDKSFLAMV94 VDIVQELKQQ104 NPRLVYVCDP 114 VLGDKWDGEG124 SMYVPEDLLP134 VYKEKVVPLA144 DIITPNQFEA154 ELLSGRKIHS 164 QEEALRVMDM174 LHSMGPDTVV184 ITSSDLPSPQ194 GSNYLIVLGS204 QRRRVVMERI 219 RMDIRKVDAV229 FVGTGDLFAA239 MLLAWTHKHP249 NNLKVACEKT259 VSTLHHVLQR 269 TIQCAKAQAG279 EGVRPSPMQL289 ELRMVQSKRD299 IEDPEIVVQA309 TVL |
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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:113 or .A:115 or .A:117 or .A:118 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:227 or .A:228 or .A:229 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
2.771
VAL115
3.812
GLY117
4.149
ASP118
3.006
THR148
4.568
ASN150
3.144
GLU153
2.791
THR186
2.481
SER187
2.716
LEU199
3.949
VAL201
3.550
ILE223
4.029
ARG224
4.196
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| Ligand Name: 5-(Hydroxymethyl)-4-(methoxymethyl)-2-methylpyridin-3-ol | Ligand Info | |||||
| Structure Description | Crystal Structure of the Ternary Human PL Kinase-Ginkgotoxin-MgATP Complex | PDB:4EN4 | ||||
| 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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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .GT0 or .GT02 or .GT03 or :3GT0;style chemicals stick;color identity;select .A:11 or .A:12 or .A:19 or .A:20 or .A:41 or .A:43 or .A:45 or .A:46 or .A:47 or .A:48 or .A:84 or .A:231 or .A:235; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: [5-Hydroxy-4-(Methoxymethyl)-6-Methylpyridin-3-Yl]methyl Dihydrogen Phosphate | Ligand Info | |||||
| Structure Description | Crystal Structure of the Ternary Human PL Kinase-Ginkgotoxin-MgATP Complex | PDB:4EN4 | ||||
| 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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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .GT1 or .GT12 or .GT13 or :3GT1;style chemicals stick;color identity;select .A:12 or .A:19 or .A:20 or .A:46 or .A:47 or .A:84 or .A:127 or .A:230 or .A:231 or .A:232 or .A:233 or .A:234 or .A:235; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| Ligand Name: Pyridoxal | Ligand Info | |||||
| Structure Description | Crystal structure of D235A mutant of human pyridoxal kinase | PDB:3FHX | ||||
| 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 .PXL or .PXL2 or .PXL3 or :3PXL;style chemicals stick;color identity;select .A:12 or .A:14 or .A:19 or .A:41 or .A:43 or .A:46 or .A:47 or .A:48 or .A:84 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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| 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 a human pyridoxal kinase | ||||
| 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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