Structure of PDB 2vgj Chain A Binding Site BS01

Receptor Information
>2vgj Chain A (length=466) Species: 72570 (Actinomadura sp. R39) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RLTELREDIDAILEDPALEGAVSGVVVVDTATGEELYSRDGGEQLLPASN
MKLFTAAAALEVLGADHSFGTEVAAESAPGRRGEVQDLYLVGRGDPTLSA
EDLDAMAAEVAASGVRTVRGDLYADDTWFDSERLVDDWWPEDEPYAYSAQ
ISALTVAHGERFDTGVTEVSVTPAAEGEPADVDLGAAEGYAELDNRAVTG
AAGSANTLVIDRPVGTNTIAVTGSLPADAAPVTALRTVDEPAALAGHLFE
EALESNGVTVKGDVGLGGVPADWQDAEVLADHTSAELSEILVPFMKFSNN
GHAEMLVKSIGQETAGAGTWDAGLVGVEEALSGLGVDTAGLVLNDGSGLS
RGNLVTADTVVDLLGQAGSAPWAQTWSASLPVAGESDPFVGGTLANRMRG
TAAEGVVEAKTGTMSGVSALSGYVPGPEGELAFSIVNNGHSGPAPLAVQD
AIAVRLAEYAGHQAPE
Ligand information
Ligand IDREC
InChIInChI=1S/C15H21N3O7S/c1-7-6-26-12(18-10(7)14(22)23)11(15(24)25)17-9(19)5-3-2-4-8(16)13(20)21/h8,11-12H,1-6,16H2,(H,17,19)(H,20,21)(H,22,23)(H,24,25)/t8-,11+,12-/m1/s1
InChIKeyJGKXEMYIHDYWCZ-JFUSQASVSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(O)C(N)CCCCC(=O)NC(C(=O)O)C1N=C(\C(=C)CS1)C(=O)O
OpenEye OEToolkits 1.5.0C=C1CS[C@@H](N=C1C(=O)O)[C@@H](C(=O)O)NC(=O)CCCC[C@H](C(=O)O)N
OpenEye OEToolkits 1.5.0C=C1CSC(N=C1C(=O)O)C(C(=O)O)NC(=O)CCCCC(C(=O)O)N
CACTVS 3.341N[CH](CCCCC(=O)N[CH]([CH]1SCC(=C)C(=N1)C(O)=O)C(O)=O)C(O)=O
CACTVS 3.341N[C@H](CCCCC(=O)N[C@@H]([C@H]1SCC(=C)C(=N1)C(O)=O)C(O)=O)C(O)=O
FormulaC15 H21 N3 O7 S
NameCEPHALOSPORIN;
(2R)-2-[(R)-{[(6R)-6-amino-6-carboxyhexanoyl]amino}(carboxy)methyl]-5-methylidene-5,6-dihydro-2H-1,3-thiazine-4-carboxy lic acid
ChEMBLCHEMBL1235646
DrugBank
ZINCZINC000058651052
PDB chain2vgj Chain A Residue 500 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2vgj Crystal Structures of Complexes of Bacterial Dd-Peptidases with Peptidoglycan-Mimetic Ligands: The Substrate Specificity Puzzle.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		S49 D142 Y147 S298 N300 R351 T411 G412 T413 S415
Binding residue
(residue number reindexed from 1)		S49 D142 Y147 S298 N300 R351 T411 G412 T413 S415
Annotation score1
Enzymatic activity
Enzyme Commision number 3.4.16.4: serine-type D-Ala-D-Ala carboxypeptidase.
Gene Ontology
Molecular Function
GO:0004180 carboxypeptidase activity
GO:0004185 serine-type carboxypeptidase activity
GO:0009002 serine-type D-Ala-D-Ala carboxypeptidase activity
Biological Process
GO:0000270 peptidoglycan metabolic process
GO:0006508 proteolysis
GO:0008360 regulation of cell shape
GO:0009252 peptidoglycan biosynthetic process
GO:0046677 response to antibiotic
GO:0071555 cell wall organization
Cellular Component
GO:0005576 extracellular region

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2vgj, PDBe:2vgj, PDBj:2vgj
PDBsum2vgj
PubMed18602645
UniProtP39045|DAC_ACTSP D-alanyl-D-alanine carboxypeptidase (Gene Name=dac)

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