PDB Entry (5dvp)
PDB ID: 5dvp Resolution: 2.18 Å Exp. Method: X-RAY DIFFRACTION
PMID: 27820797 DOI: 10.1038/nchembio.2237
Protein
Protein Name: L,D-transpeptidase 2
Uniprot ID/ACC: I6Y9J2 (LDT2_MYCTU) Organism: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Gene Symbol: ldtB Gene ID: 888160
Protein Class: TRANSFERASE
Ligand
Ligand Name:   doripenem
Canonical SMILES:   C[C@@H](O)[C@@H]1[C@H]2[C@@H](C)C(S[C@@H]3CN[C@H](CNS(N)(=O)=O)C3)=C(N2C1=O)C(O)=O
Standard InChI:   InChI=1S/C15H24N4O6S2/c1-6-11-10(7(2)20)14(21)19(11)12(15(22)23)13(6)26-9-3-8(17-5-9)4-18-27(16,24)25/h6-11,17-18,20H,3-5H2,1-2H3,(H,22,23)(H2,16,24,25)/t6-,7-,8+,9+,10-,11-/m1/s1
HET Code:   DRW PubChem:   73303
DrugBank:   DB06211 ChEMBL:   CHEMBL491571
Molecular Formula:   C15H24N4O6S2 Mol. Weight:   420.11374 logP:   -1.6031
HBD:   5 HBA:   7
#Rotatable Bonds:   7 TPSA:   162.06
Covalent Mechanism
Reaction Name Residue Chain ID SASA pKa Warhead Name Warhead Structure
Beta-Lactam Addition CYS 354 A 8.29 11.81 Beta-Lactam
Binding Affinity
-