PDB Entry (2y59) |
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PDB ID: 2y59 | Resolution: 2.5 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: 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 |
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Database Name | Value |
PDBBind | Ki : 360 nM |