PDB Entry (2y59)
PDB ID: 2y59 Resolution: 2.5 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:   DIHYDROXY-[[(2-NITROPHENYL)CARBONYLAMINO]METHYL]BORON
Canonical SMILES:   OB(O)CNC(=O)c1ccccc1[N+]([O-])=O
Standard InChI:   InChI=1S/C8H9BN2O5/c12-8(10-5-9(13)14)6-3-1-2-4-7(6)11(15)16/h1-4,13-14H,5H2,(H,10,12)
HET Code:   ZA3 PubChem:   66561495
DrugBank:   - ChEMBL:   CHEMBL2035292
Molecular Formula:   C8H9BN2O5 Mol. Weight:   224.06046 logP:   -0.6634
HBD:   3 HBA:   5
#Rotatable Bonds:   4 TPSA:   112.7
Covalent Mechanism
Reaction Name Residue Chain ID SASA pKa Warhead Name Warhead Structure
Composite Reaction LYS 410 B 0.26 - Boronic Acid
Composite Reaction SER 298 B 24.07 - Boronic Acid
Composite Reaction SER 49 B 16.71 - Boronic Acid
Binding Affinity
Database Name Value
PDBBind Ki : 360 nM