PDB Entry (5dzp)
PDB ID: 5dzp Resolution: 2.19 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:   Carbapenem T206
Canonical SMILES:   CCCOC(=O)CSC1=C(N2[C@@H]([C@@H]([C@@H](C)O)C2=O)[C@H]1C)C(O)=O
Standard InChI:   InChI=1S/C15H21NO6S/c1-4-5-22-9(18)6-23-13-7(2)11-10(8(3)17)14(19)16(11)12(13)15(20)21/h7-8,10-11,17H,4-6H2,1-3H3,(H,20,21)/t7-,8-,10-,11-/m1/s1
HET Code:   6B7 PubChem:   122174203
DrugBank:   - ChEMBL:   -
Molecular Formula:   C15H21NO6S Mol. Weight:   343.10895 logP:   0.8265
HBD:   2 HBA:   6
#Rotatable Bonds:   7 TPSA:   104.14
Covalent Mechanism
Reaction Name Residue Chain ID SASA pKa Warhead Name Warhead Structure
Beta-Lactam Addition CYS 354 A 18.63 11.79 Beta-Lactam
Binding Affinity
-