Structure of PDB 6g59 Chain A Binding Site BS01

Receptor Information
>6g59 Chain A (length=387) Species: 158878 (Staphylococcus aureus subsp. aureus Mu50) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YKKAGFSDKYYRSAYMNVDLNAVASNFKVFSTLHPNKTVMAVVKANAYGL
GSVKVARHLMENGATFFAVATLDEAIELRMHGITAKILVLGVLPAKDIDK
AIQHRVALTVPSKQWLKEAIKNISGEQEKKLWLHIKLDTGMGRLGIKDTN
TYQEVIEIIQQYEQLVFEGVFTHFACADEPGDMTTEQYQRFKDMVNEAIK
PEYIHCQNSAGSLLMDCQFCNAIRPGISLYGYYPSEYVQQKVKVHLKPSV
QLIANVVQTKTLQAGESVSYGATYTATDPTTIALLPIGYADGYLRIMQGS
FVNVNGHQCEVIGRVCMDQTIVKVPDQVKAGDSVILIDNHRESPQSVEVV
AEKQHTINYEVLCNLSRRLPRIYHDGDQRFVTNELLK
Ligand information
Ligand IDEM2
InChIInChI=1S/C9H8NO6P/c1-2-8-9(12)7(4-11)6(3-10-8)5-16-17(13,14)15/h1,3-4,12H,5H2,(H2,13,14,15)
InChIKeyOAIRLJMOEFCXML-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Oc1c(C=O)c(CO[P](O)(O)=O)cnc1C#C
OpenEye OEToolkits 2.0.6C#Cc1c(c(c(cn1)COP(=O)(O)O)C=O)O
FormulaC9 H8 N O6 P
Name(6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate
ChEMBL
DrugBank
ZINC
PDB chain6g59 Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6g59 Mining the cellular inventory of pyridoxal phosphate-dependent enzymes with functionalized cofactor mimics.
Resolution2.45 Å
Binding residue
(original residue number in PDB)		K39 Y43 L85 H168 S204 R219 G221 I222 Y354
Binding residue
(residue number reindexed from 1)		K44 Y48 L90 H173 S209 R224 G226 I227 Y359
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) K39 R138 H168 R219 Y265 C311 D313
Catalytic site (residue number reindexed from 1) K44 R143 H173 R224 Y270 C316 D318
Enzyme Commision number 5.1.1.1: alanine racemase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0008784 alanine racemase activity
GO:0016853 isomerase activity
GO:0030170 pyridoxal phosphate binding
Biological Process
GO:0006522 alanine metabolic process
GO:0009252 peptidoglycan biosynthetic process
GO:0030632 D-alanine biosynthetic process
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:6g59, PDBe:6g59, PDBj:6g59
PDBsum6g59
PubMed30297752
UniProtP63479|ALR1_STAAM Alanine racemase 1 (Gene Name=alr1)

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