Structure of PDB 3vmm Chain A Binding Site BS04

Receptor Information
>3vmm Chain A (length=471) Species: 1423 (Bacillus subtilis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ERKTVLVIADLGGCPPHMFYKSAAEKYNLVSFIPRPFAITASHAALIEKY
SVAVIKDKDYFKSLADFEHPDSIYWAHEDHNKPEEEVVEQIVKVAEMFGA
DAITTNNELFIAPMAKACERLGLRGAGVQAAENARDKNKMRDAFNKAGVK
SIKNKRVTTLEDFRAALEEIGTPLILKPTYLASSIGVTLITDTETAEDEF
NRVNDYLKSINVPKAVTFEAPFIAEEFLQGEYGDWYQTEGYSDYISIEGI
MADGEYFPIAIHDKTPQIGFTETSHITPSILDEEAKKKIVEAAKKANEGL
GLQNCATHTEIKLMKNREPGLIESAARFAGWNMIPNIKKVFGLDMAQLLL
DVLCFGKDADLPDGLLDQEPYYVADCHLYPQHFKQNGQIPETAEDLVIEA
IDIPDGLLKGDTEIVSFSAAAPGTSVDLTLFEAFNSIAAFELKGSNSQDV
AESIRQIQQHAKLTAKYVLPV
Ligand information
Ligand IDP0D
InChIInChI=1S/C12H19NO7P2/c1-9(13)21(16,20-22(17,18)19)8-11(12(14)15)7-10-5-3-2-4-6-10/h2-6,9,11H,7-8,13H2,1H3,(H,14,15)(H2,17,18,19)/t9-,11-,21+/m1/s1
InChIKeyKXASHFLSUHEZCK-UODZXCQVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CC(N)P(=O)(CC(Cc1ccccc1)C(=O)O)OP(=O)(O)O
CACTVS 3.370C[CH](N)[P](=O)(C[CH](Cc1ccccc1)C(O)=O)O[P](O)(O)=O
CACTVS 3.370C[C@H](N)[P@](=O)(C[C@@H](Cc1ccccc1)C(O)=O)O[P](O)(O)=O
ACDLabs 12.01O=C(O)C(CP(=O)(OP(=O)(O)O)C(N)C)Cc1ccccc1
OpenEye OEToolkits 1.7.6C[C@H](N)[P@](=O)(C[C@@H](Cc1ccccc1)C(=O)O)OP(=O)(O)O
FormulaC12 H19 N O7 P2
Name(2S)-3-[(S)-[(1R)-1-aminoethyl](phosphonooxy)phosphoryl]-2-benzylpropanoic acid
ChEMBL
DrugBank
ZINCZINC000098209279
PDB chain3vmm Chain A Residue 504 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3vmm Structural and enzymatic characterization of BacD, an l-amino acid dipeptide ligase from Bacillus subtilis
Resolution2.5 Å
Binding residue
(original residue number in PDB)		L12 G13 G14 S184 E273 H309 E311 E324 R328 G331
Binding residue
(residue number reindexed from 1)		L11 G12 G13 S183 E272 H308 E310 E323 R327 G330
Annotation score1
Enzymatic activity
Enzyme Commision number 6.3.2.49: L-alanine--L-anticapsin ligase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0005524 ATP binding
GO:0016874 ligase activity
GO:0034026 L-amino-acid alpha-ligase activity
GO:0046872 metal ion binding
Biological Process
GO:0017000 antibiotic biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3vmm, PDBe:3vmm, PDBj:3vmm
PDBsum3vmm
PubMed22407814
UniProtP39641|BACD_BACSU Alanine--anticapsin ligase (Gene Name=bacD)

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