Structure of PDB 4lut Chain B Binding Site BS01

Receptor Information
>4lut Chain B (length=364) Species: 272563 (Clostridioides difficile 630) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KITVPTWAEINLDNLRFNLNNIKNLLEEDIKICGVIKADAYGHGAVEVAK
LLEKEKVDYLAVARTAEGIELRQNGITLPILNLGYTPDEAFEDSIKNKIT
MTVYSLETAQKINEIAKSLGEKACVHVKIDSGMTRIGFQPNEESVQEIIE
LNKLEYIDLEGMFTHFATADEVSKEYTYKQANNYKFMSDKLDEAGVKIAI
KHVSNSAAIMDCPDLRLNMVRAGIILYGHYPSDDVFKDRLELRPAMKLKS
KIGHIKQETIATVPIGYADGFTRIQKNPKVLIKGEVFDVVGRICMDQIMV
RIDKDIDIKVGDEVILFGEGEVTAERIAKDLGTINYEVLCMISRRVDRVY
MENNELVQINSYLL
Ligand information
Ligand IDDCS
InChIInChI=1S/C11H16N3O7P/c1-6-10(15)8(3-13-9-5-20-14-11(9)16)7(2-12-6)4-21-22(17,18)19/h2,9,13,15H,3-5H2,1H3,(H,14,16)(H2,17,18,19)/t9-/m1/s1
InChIKeyNNRZSZJOQKAGTO-SECBINFHSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H]2CONC2=O)O
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)COP(=O)(O)O)CNC2CONC2=O)O
CACTVS 3.341Cc1ncc(CO[P](O)(O)=O)c(CN[C@@H]2CONC2=O)c1O
CACTVS 3.341Cc1ncc(CO[P](O)(O)=O)c(CN[CH]2CONC2=O)c1O
ACDLabs 10.04O=C2NOCC2NCc1c(cnc(c1O)C)COP(=O)(O)O
FormulaC11 H16 N3 O7 P
NameD-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-N,O-CYCLOSERYLAMIDE;
D-PYRIDOXYL-N,O-CYCLOSERYLAMIDE-5-MONOPHOSPHATE
ChEMBL
DrugBankDB02038
ZINCZINC000002043174
PDB chain4lut 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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PDB4lut Structural and biochemical analyses of alanine racemase from the multidrug-resistant Clostridium difficile strain 630.
Resolution2.26 Å
Binding residue
(original residue number in PDB)
Y287 M315
Binding residue
(residue number reindexed from 1)
Y267 M295
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) K39 R137 H167 R223 C314 D316
Catalytic site (residue number reindexed from 1) K37 R135 H165 R221 C294 D296
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:4lut, PDBe:4lut, PDBj:4lut
PDBsum4lut
PubMed25004969
UniProtQ180W0

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