Structure of PDB 2vd9 Chain A Binding Site BS04

Receptor Information
>2vd9 Chain A (length=386) Species: 198094 (Bacillus anthracis str. Ames) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
APFYRDTWVEVDLDAIYNNVTHIKEFIPSDVEIFAVVKGNAYGHDYVPVA
KIALEAGATRLAVAFLDEALVLRRAGITAPILVLGPSPPRDINVAAENDV
ALTVFQKEWVDEAIKLWDGSSTMKYHINFDSGMGRIGIRERKELKGFLKS
LEGAPFLELEGVYTHFATADEVETSYFDKQYNTFLEQLSWLKEFGVDPKF
VHTANSAATLRFQGITFNAVRIGIAMYGLSPSVEIRPFLPFKLEPALSLH
TKVAHIKQVIKGDGISYNVTYRTKTEEWIATVAIGYADGWLRRLQGFEVL
VNGKRVPIVGRVTMDQFMIHLPCEVPLGTKVTLIGRQGDEYISATEVAEY
SGTINYEIITTISFRVPRIFIRNGKVVEVINYLNDI
Ligand information
Ligand IDIN5
InChIInChI=1S/C10H18N2O8P2/c1-6-10(13)9(4-12-7(2)21(14,15)16)8(3-11-6)5-20-22(17,18)19/h3,7,12-13H,4-5H2,1-2H3,(H2,14,15,16)(H2,17,18,19)/t7-/m1/s1
InChIKeyWHDCJKAOZPBUAY-SSDOTTSWSA-N
SMILES
SoftwareSMILES
CACTVS 3.341C[CH](NCc1c(O)c(C)ncc1CO[P](O)(O)=O)[P](O)(O)=O
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)COP(=O)(O)O)CNC(C)P(=O)(O)O)O
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H](C)P(=O)(O)O)O
CACTVS 3.341C[C@H](NCc1c(O)c(C)ncc1CO[P](O)(O)=O)[P](O)(O)=O
ACDLabs 10.04O=P(O)(O)OCc1cnc(c(O)c1CNC(C)P(=O)(O)O)C
FormulaC10 H18 N2 O8 P2
Name{1-[(3-HYDROXY-METHYL-5-PHOSPHONOOXY-METHYL-PYRIDIN-4-YLMETHYL)-AMINO]-ETHYL}-PHOSPHONIC ACID
ChEMBL
DrugBankDB03327
ZINCZINC000002047885
PDB chain2vd9 Chain B Residue 1392 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2vd9 Structures of an Alanine Racemase from Bacillus Anthracis (Ba0252) in the Presence and Absence of (R)-1-Aminoethylphosphonic Acid (L-Ala-P).
Resolution2.1 Å
Binding residue
(original residue number in PDB)		Y270 T316 M317
Binding residue
(residue number reindexed from 1)		Y267 T313 M314
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) K41 R138 H168 R224 Y270 T316 D318
Catalytic site (residue number reindexed from 1) K38 R135 H165 R221 Y267 T313 D315
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
GO:0046872 metal ion 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:2vd9, PDBe:2vd9, PDBj:2vd9
PDBsum2vd9
PubMed18453697
UniProtA0A6L7HC45

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