PDB Entry (4a52)
PDB ID: 4a52 Resolution: - Exp. Method: SOLUTION NMR
PMID: 22579252 DOI: 10.1016/J.STR.2012.03.015
Protein
Protein Name: Putative L,D-transpeptidase YkuD
Uniprot ID/ACC: O34816 (YKUD_BACSU) Organism: Bacillus subtilis (strain 168)
Gene Symbol: ykuD Gene ID: 939216
Protein Class: TRANSFERASE
Ligand
Ligand Name:   Imipenem
Canonical SMILES:   C[C@@H](O)[C@@H]1[C@H]2CC(SCCNC=N)=C(N2C1=O)C(O)=O
Standard InChI:   InChI=1S/C12H17N3O4S/c1-6(16)9-7-4-8(20-3-2-14-5-13)10(12(18)19)15(7)11(9)17/h5-7,9,16H,2-4H2,1H3,(H2,13,14)(H,18,19)/t6-,7-,9-/m1/s1
HET Code:   IM2 PubChem:   104838
DrugBank:   DB01598 ChEMBL:   CHEMBL148
Molecular Formula:   C12H17N3O4S Mol. Weight:   299.09396 logP:   -0.17603
HBD:   4 HBA:   5
#Rotatable Bonds:   7 TPSA:   113.72
Covalent Mechanism
Reaction Name Residue Chain ID SASA pKa Warhead Name Warhead Structure
Beta-Lactam Addition CYS 142 A 34.22 10.97 Beta-Lactam
Binding Affinity
-