PDB Entry (3zvw)
PDB ID: 3zvw Resolution: 2.0 Å Exp. Method: X-RAY DIFFRACTION
PMID: 21574608 DOI: 10.1021/JA200696Y
Protein
Protein Name: D-alanyl-D-alanine carboxypeptidase
Uniprot ID/ACC: P39045 (DAC_ACTSP) Organism: Actinomadura sp. (strain R39)
Gene Symbol: dac Gene ID: -
Protein Class: HYDROLASE
Ligand
Ligand Name:   PHENYLACETAMIDOMETHYL BORONIC ACID
Canonical SMILES:   OB(O)CNC(=O)Cc1ccccc1
Standard InChI:   InChI=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)
HET Code:   FP5 PubChem:   9920615
DrugBank:   - ChEMBL:   CHEMBL1275918
Molecular Formula:   C9H12BNO3 Mol. Weight:   193.09102 logP:   -0.6427
HBD:   3 HBA:   3
#Rotatable Bonds:   4 TPSA:   69.56
Covalent Mechanism
Reaction Name Residue Chain ID SASA pKa Warhead Name Warhead Structure
Composite Reaction LYS 410 B 0.23 4.03 Boronic Acid
Composite Reaction SER 298 B 22.51 - Boronic Acid
Composite Reaction SER 49 B 16.55 - Boronic Acid
Binding Affinity
Database Name Value
PDBBind Ki : 125000 nM
BindingDB Ki : 125000 nM , IC50 : 320000 nM