Structure of PDB 2ex9 Chain A Binding Site BS01

Receptor Information
>2ex9 Chain A (length=442) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TQLPAGANLALMVQKVGASAPAIDYHSQQMALPASTQKVITALAALIQLG
PDFRFTTTLETKGNVENGVLKGDLVARFGADPTLKRQDIRNMVATLKKSG
VNQIDGNVLIDTSIFASHDKAPGWPWNDMTQCFSAPPAAAIVDRNCFSVS
LYSAPKPGDMAFIRVASYYPVTMFSQVRTLPRGSAEAQYCELDVVPGDLN
RFTLTGCLPQRSEPLPLAFAVQDGASYAGAILKYELKQAGITWSGTLLRQ
TQVNEPGTVVASKQSAPLHDLLKIMLKKSDNMIADTVFRMIGHARFNVPG
TWRAGSDAVRQILRQQAGVDIGNTIIADGSGLSRHNLIAPATMMQVLQYI
AQHDNELNFISMLPLAGYDGSLQYRAGLHQAGVDGKVSAKTGSLQGVYNL
AGFITTASGQRMAFVQYLSGYAVEIPLVRFESRLYKDIYQNN
Ligand information
Ligand ID35P
InChIInChI=1S/C16H20N2O5S/c1-16(2)13(15(21)22)18-14(24-16)11(8-19)17-12(20)9-23-10-6-4-3-5-7-10/h3-8,11,13-14,18H,9H2,1-2H3,(H,17,20)(H,21,22)/t11-,13+,14-/m1/s1
InChIKeyOQVOJWZOUWGSDX-KWCYVHTRSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC1(C)S[CH](N[CH]1C(O)=O)[CH](NC(=O)COc2ccccc2)C=O
CACTVS 3.385CC1(C)S[C@@H](N[C@H]1C(O)=O)[C@H](NC(=O)COc2ccccc2)C=O
ACDLabs 12.01c1c(cccc1)OCC(=O)NC(C2NC(C(S2)(C)C)C(O)=O)C=O
OpenEye OEToolkits 1.7.6CC1(C(NC(S1)C(C=O)NC(=O)COc2ccccc2)C(=O)O)C
OpenEye OEToolkits 1.7.6CC1([C@@H](N[C@H](S1)[C@@H](C=O)NC(=O)COc2ccccc2)C(=O)O)C
FormulaC16 H20 N2 O5 S
Name(2R,4S)-5,5-dimethyl-2-{(1R)-2-oxo-1-[(phenoxyacetyl)amino]ethyl}-1,3-thiazolidine-4-carboxylic acid;
OPEN FORM - PENICILLIN V
ChEMBL
DrugBank
ZINCZINC000016051987
PDB chain2ex9 Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2ex9 Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli, both in the native form and covalently linked to various antibiotics
Resolution1.65 Å
Binding residue
(original residue number in PDB)		S62 S306 N308 S420 L421
Binding residue
(residue number reindexed from 1)		S35 S279 N281 S393 L394
Annotation score1
Enzymatic activity
Enzyme Commision number 3.4.16.4: serine-type D-Ala-D-Ala carboxypeptidase.
3.4.21.-
Gene Ontology
Molecular Function
GO:0004175 endopeptidase activity
GO:0004180 carboxypeptidase activity
GO:0004185 serine-type carboxypeptidase activity
GO:0004252 serine-type endopeptidase activity
GO:0005515 protein binding
GO:0008658 penicillin binding
GO:0009002 serine-type D-Ala-D-Ala carboxypeptidase activity
GO:0016787 hydrolase activity
Biological Process
GO:0000270 peptidoglycan metabolic process
GO:0006508 proteolysis
GO:0008360 regulation of cell shape
GO:0009252 peptidoglycan biosynthetic process
GO:0043093 FtsZ-dependent cytokinesis
GO:0046677 response to antibiotic
GO:0051301 cell division
GO:0071555 cell wall organization
Cellular Component
GO:0005886 plasma membrane
GO:0042597 periplasmic space

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2ex9, PDBe:2ex9, PDBj:2ex9
PDBsum2ex9
PubMed16411754
UniProtP24228|DACB_ECOLI D-alanyl-D-alanine carboxypeptidase DacB (Gene Name=dacB)

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