PDB Entry (3zvw) |
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PDB ID: 3zvw | Resolution: 2.0 Å | Exp. Method: X-RAY DIFFRACTION |
PMID: 21574608 | DOI: 10.1021/JA200696Y | |
Protein |
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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 |
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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 |
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Database Name | Value |
PDBBind | Ki : 125000 nM |
BindingDB | Ki : 125000 nM , IC50 : 320000 nM |