Structure of PDB 1vfs Chain B Binding Site BS02

Receptor Information
>1vfs Chain B (length=382) Species: 1914 (Streptomyces lavendulae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ETPTRVYAEIDLDAVRANVRALRARAPRSALMAVVKSNAYGHGAVPCARA
AQEAGAAWLGTATPEEALELRAAGIQGRIMCWLWTPGGPWREAIETDIDV
SVSGMWALDEVRAAARAAGRTARIQLKADTGLGRNGCQPADWAELVGAAV
AAQAEGTVQVTGVWSHFACADEPGHPSIRLQLDAFRDMLAYAEKEGVDPE
VRHIANSPATLTLPETHFDLVRTGLAVYGVSPSPELGTPAQLGLRPAMTL
RASLALVKTVPAGHGVSYGHHYVTESETHLALVPAGYADGIPRNASGRGP
VLVAGKIRRAAGRIAMDQFVVDLGEDLAEAGDEAVILGDAERGEPTAEDW
AQAAHTIAYEIVTRIGGRVPRVYLGGLEHHHH
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 chain1vfs Chain B Residue 1401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1vfs Structural evidence that alanine racemase from a D-cycloserine-producing microorganism exhibits resistance to its own product.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		K1038 Y1042 W1084 R1136 H1168 S1209 R1224 G1226 L1227 Y1361
Binding residue
(residue number reindexed from 1)		K36 Y40 W82 R134 H166 S207 R222 G224 L225 Y359
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) K1038 R1136 H1168 R1224 Y1270 A1317 D1319
Catalytic site (residue number reindexed from 1) K36 R134 H166 R222 Y268 A315 D317
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:1vfs, PDBe:1vfs, PDBj:1vfs
PDBsum1vfs
PubMed15302886
UniProtQ65YW7

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