PDB Entry (2y2i)
PDB ID: 2y2i Resolution: 1.78 Å Exp. Method: X-RAY DIFFRACTION
PMID: 21732689 DOI: 10.1021/CB2001846
Protein
Protein Name: DD-transpeptidase
Uniprot ID/ACC: Q7CRA4 (Q7CRA4_STRR6) Organism: Streptococcus pneumoniae (strain ATCC BAA-255 / R6)
Gene Symbol: pbp1b Gene ID: -
Protein Class: TRANSFERASE
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
Borylation SER 460 A 10.98 - Boronic Acid
Binding Affinity
Database Name Value
PDBBind IC50 : 26000 nM