Structure of PDB 4ywr Chain A Binding Site BS01

Receptor Information
>4ywr Chain A (length=228) Species: 1116234 (Acinetobacter baumannii AB5075) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RPTVLCFSGLDPSGGAGLQADIEAIGQSGAHAAIACTALTIQNSQQVFGF
EATSKELLLAQANAVVGDLPIKCVKSGMLGTTDNIAALAEFLRAHPDYQY
VLDPVLVANSGGSLGDQATLVKAFVELIPLATLITPNTVELRALTGVTDL
DQATQKLFEMGAKAVLVKGGHEDTPDFIKNSLYIDGELAASSTCPRCSLA
SFIAGRLALGDSLKIAVQHAETWLFGVL
Ligand information
Ligand IDPLP
InChIInChI=1S/C8H10NO6P/c1-5-8(11)7(3-10)6(2-9-5)4-15-16(12,13)14/h2-3,11H,4H2,1H3,(H2,12,13,14)
InChIKeyNGVDGCNFYWLIFO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1ncc(CO[P](O)(O)=O)c(C=O)c1O
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)COP(=O)(O)O)C=O)O
ACDLabs 10.04O=P(O)(O)OCc1cnc(c(O)c1C=O)C
FormulaC8 H10 N O6 P
NamePYRIDOXAL-5'-PHOSPHATE;
VITAMIN B6 Phosphate
ChEMBLCHEMBL82202
DrugBankDB00114
ZINCZINC000001532514
PDB chain4ywr Chain A Residue 300 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4ywr Structure of a putative phosphomethylpyrimidine kinase from Acinetobacter baumannii in non-covalent complex with pyridoxal phosphate.
Resolution1.65 Å
Binding residue
(original residue number in PDB)		A25 G26 Q51 M87 D112 A117 N118 L123 S216
Binding residue
(residue number reindexed from 1)		A16 G17 Q42 M78 D103 A108 N109 L114 S198
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) K177 C215
Catalytic site (residue number reindexed from 1) K168 C197
Enzyme Commision number 2.7.1.49: hydroxymethylpyrimidine kinase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0005524 ATP binding
GO:0008902 hydroxymethylpyrimidine kinase activity
GO:0008972 phosphomethylpyrimidine kinase activity
GO:0016301 kinase activity
Biological Process
GO:0009228 thiamine biosynthetic process
GO:0009229 thiamine diphosphate biosynthetic process
GO:0016310 phosphorylation
Cellular Component
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:4ywr, PDBe:4ywr, PDBj:4ywr
PDBsum4ywr
PubMed38306231
UniProtA0A0J9X285|HMPK_ACIB6 Hydroxylmethylpyrimidine kinase (Gene Name=ACINIS123_0279)

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