Structure of PDB 2y55 Chain D Binding Site BS01

Receptor Information
>2y55 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 IDFP5
InChIInChI=1S/C9H12BNO3/c12-9(11-7-10(13)14)6-8-4-2-1-3-5-8/h1-5,13-14H,6-7H2,(H,11,12)
InChIKeyWPZJZIUTEZTIJI-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.6.1B(CNC(=O)Cc1ccccc1)(O)O
CACTVS 3.352OB(O)CNC(=O)Cc1ccccc1
FormulaC9 H12 B N O3
NamePHENYLACETAMIDOMETHYL BORONIC ACID
ChEMBLCHEMBL1275918
DrugBank
ZINCZINC000169879812
PDB chain2y55 Chain D Residue 500 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2y55 Unexpected Tricovalent Binding Mode of Boronic Acids within the Active Site of a Penicillin- Binding Protein.
Resolution2.6 Å
Binding residue
(original residue number in PDB)		S49 K52 S298 N300 K410 T411 T413 M414
Binding residue
(residue number reindexed from 1)		S49 K52 S298 N300 K410 T411 T413 M414
Annotation score1
Binding affinityBindingDB: Ki=125000nM,IC50=320000nM
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:2y55, PDBe:2y55, PDBj:2y55
PDBsum2y55
PubMed21574608
UniProtP39045|DAC_ACTSP D-alanyl-D-alanine carboxypeptidase (Gene Name=dac)

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