Structure of PDB 6yk0 Chain D Binding Site BS01

Receptor Information
>6yk0 Chain D (length=309) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ECRVLSIQSHVVRGYVGNRAAMFPLQVLGFEVDAVNSVQFSNHTGYAHWK
GQVLKSQELHELYEGLKVNDVNKYDYVLTGYTRDKSFLAMVVDIVRELKQ
QNSRLVYVCDPVMGDKWNGEGSMYVPQDLLPVYRDKVVPVADIITPNQFE
AELLSGRKIHSQEEAFEVMDMLHCMGPDTVVITSSDLPSSQGSDYLIALG
SQRMRKPDGSTVTQRIRMEMRKVEAVFVGTGDLFAAMLLAWTHKHPDNLK
VACEKTVSAMQHVLQRTIRCAKAEAGEGQKPSPAQLELRMVQSKRDIEDP
EIVVQATVL
Ligand information
Ligand IDAGS
InChIInChI=1S/C10H16N5O12P3S/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(25-10)1-24-28(18,19)26-29(20,21)27-30(22,23)31/h2-4,6-7,10,16-17H,1H2,(H,18,19)(H,20,21)(H2,11,12,13)(H2,22,23,31)/t4-,6-,7-,10-/m1/s1
InChIKeyNLTUCYMLOPLUHL-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=S)(O)O)O)O)N
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[C@@H](O)[C@H]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[CH](O)[CH]3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=S)(O)O)O)O)N
ACDLabs 12.01O=P(O)(OP(=S)(O)O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
FormulaC10 H16 N5 O12 P3 S
NamePHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER;
ATP-GAMMA-S;
ADENOSINE 5'-(3-THIOTRIPHOSPHATE);
ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE);
ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE
ChEMBLCHEMBL131890
DrugBankDB02930
ZINCZINC000008295128
PDB chain6yk0 Chain D Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6yk0 Pyridoxal kinase inhibition by artemisinins down-regulates inhibitory neurotransmission.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		D118 N150 E153 T186 S187 M223 V226 T233 G234 F237 L267
Binding residue
(residue number reindexed from 1)		D115 N147 E150 T183 S184 M220 V223 T230 G231 F234 L264
Annotation score4
Enzymatic activity
Enzyme Commision number 2.7.1.35: pyridoxal kinase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0005524 ATP binding
GO:0008270 zinc ion binding
GO:0008478 pyridoxal kinase activity
GO:0016301 kinase activity
GO:0016773 phosphotransferase activity, alcohol group as acceptor
GO:0030170 pyridoxal phosphate binding
GO:0030955 potassium ion binding
GO:0031402 sodium ion binding
GO:0031403 lithium ion binding
GO:0042803 protein homodimerization activity
GO:0046872 metal ion binding
Biological Process
GO:0008614 pyridoxine metabolic process
GO:0009443 pyridoxal 5'-phosphate salvage
GO:0016310 phosphorylation
GO:0042816 vitamin B6 metabolic process
GO:0042817 pyridoxal metabolic process
GO:0042818 pyridoxamine metabolic process
GO:0042822 pyridoxal phosphate metabolic process
Cellular Component
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6yk0, PDBe:6yk0, PDBj:6yk0
PDBsum6yk0
PubMed33318193
UniProtQ8K183|PDXK_MOUSE Pyridoxal kinase (Gene Name=Pdxk)

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