Structure of PDB 6yk1 Chain A Binding Site BS01

Receptor Information
>6yk1 Chain A (length=305) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ECRVLSIQSHVVRGYVGNRAAMFPLQVLGFEVDAVNSVQFSNHTGYAHWK
GQVLKSQELHELYEGLKVNDVNKYDYVLTGYTRDKSFLAMVVDIVRELKQ
QNSRLVYVCDPVMGDKGSMYVPQDLLPVYRDKVVPVADIITPNQFEAELL
SGRKIHSQEEAFEVMDMLHCMGPDTVVITSSDLPSSQGSDYLIALGSQRM
RKPDGSTVTQRIRMEMRKVEAVFVGTGDLFAAMLLAWTHKHPDNLKVACE
KTVSAMQHVLQRTIRCAKAEAGEGQKPSPAQLELRMVQSKRDIEDPEIVV
QATVL
Ligand information
Ligand IDD95
InChIInChI=1S/C19H28O8/c1-10-4-5-13-11(2)16(23-15(22)7-6-14(20)21)24-17-19(13)12(10)8-9-18(3,25-17)26-27-19/h10-13,16-17H,4-9H2,1-3H3,(H,20,21)/t10-,11-,12+,13+,16-,17-,18-,19-/m1/s1
InChIKeyFIHJKUPKCHIPAT-AHIGJZGOSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6C[C@@H]1CC[C@H]2[C@H]([C@@H](O[C@H]3[C@@]24[C@H]1CC[C@](O3)(OO4)C)OC(=O)CCC(=O)O)C
CACTVS 3.385C[CH]1CC[CH]2[CH](C)[CH](O[CH]3O[C]4(C)CC[CH]1[C]23OO4)OC(=O)CCC(O)=O
OpenEye OEToolkits 2.0.6CC1CCC2C(C(OC3C24C1CCC(O3)(OO4)C)OC(=O)CCC(=O)O)C
CACTVS 3.385C[C@@H]1CC[C@H]2[C@@H](C)[C@@H](O[C@@H]3O[C@@]4(C)CC[C@@H]1[C@@]23OO4)OC(=O)CCC(O)=O
FormulaC19 H28 O8
NameArtesunate
ChEMBLCHEMBL361497
DrugBankDB09274
ZINCZINC000014096305
PDB chain6yk1 Chain A Residue 503 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB6yk1 Pyridoxal kinase inhibition by artemisinins down-regulates inhibitory neurotransmission.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		F43 T47 Y84 R86 D87
Binding residue
(residue number reindexed from 1)		F40 T44 Y81 R83 D84
Annotation score1
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6yk1, PDBe:6yk1, PDBj:6yk1
PDBsum6yk1
PubMed33318193
UniProtQ8K183|PDXK_MOUSE Pyridoxal kinase (Gene Name=Pdxk)

[Back to BioLiP]