Structure of PDB 1w8y Chain D Binding Site BS02

Receptor Information
>1w8y Chain D (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 IDNCF
InChIInChI=1S/C13H14N2O5S2/c16-9(6-7-2-1-4-21-7)15-10(13(19)20)11-14-8(12(17)18)3-5-22-11/h1-2,4,10-11H,3,5-6H2,(H,15,16)(H,17,18)(H,19,20)/t10-,11+/m0/s1
InChIKeyLNPNJPUNJYVKHH-WDEREUQCSA-N
SMILES
SoftwareSMILES
CACTVS 3.385OC(=O)[CH](NC(=O)Cc1sccc1)[CH]2SCCC(=N2)C(O)=O
ACDLabs 12.01S1CCC(C(O)=O)=NC1C(C=O)NC(=O)Cc2cccs2
OpenEye OEToolkits 2.0.7c1cc(sc1)CC(=O)N[C@@H]([C@@H]2N=C(CCS2)C(=O)O)C(=O)O
OpenEye OEToolkits 2.0.7c1cc(sc1)CC(=O)NC(C2N=C(CCS2)C(=O)O)C(=O)O
CACTVS 3.385OC(=O)[C@@H](NC(=O)Cc1sccc1)[C@H]2SCCC(=N2)C(O)=O
FormulaC13 H14 N2 O5 S2
Name(2R)-2-{(1R)-2-OXO-1-[(2-THIENYLACETYL)AMINO]ETHYL}-5,6-DIHYDRO-2H-1,3-THIAZINE-4-CARBOXYLIC ACID;
NITROCEFIN, open form without dinitrophenyl-ethenyl group;
(2R)-2-[(1R)-2-oxo-1-{[(thiophen-2-yl)acetyl]amino}ethyl]-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid
ChEMBL
DrugBank
ZINC
PDB chain1w8y Chain D Residue 520 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1w8y Crystal Structure of the Actinomadura R39 Dd- Peptidase Reveals New Domains in Penicillin- Binding Proteins.
Resolution2.4 Å
Binding residue
(original residue number in PDB)
S49 D142 Y147 S298 N300 L349 T411 G412 T413
Binding residue
(residue number reindexed from 1)
S49 D142 Y147 S298 N300 L349 T411 G412 T413
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:1w8y, PDBe:1w8y, PDBj:1w8y
PDBsum1w8y
PubMed15987687
UniProtP39045|DAC_ACTSP D-alanyl-D-alanine carboxypeptidase (Gene Name=dac)

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