PDB Entry (5dcc)
PDB ID: 5dcc Resolution: 2.45 Å Exp. Method: X-RAY DIFFRACTION
PMID: 28545389 DOI: 10.1186/s12858-017-0082-4
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:   BIAPENEM
Canonical SMILES:   C[C@@H](O)[C@@H]1[C@H]2[C@@H](C)C(S[C@H]3Cn4cnc[n+]4C3)=C(N2C1=O)C(O)=O
Standard InChI:   InChI=1S/C15H18N4O4S/c1-7-11-10(8(2)20)14(21)19(11)12(15(22)23)13(7)24-9-3-17-5-16-6-18(17)4-9/h5-11,20H,3-4H2,1-2H3/p+1/t7-,8-,10-,11-/m1/s1
HET Code:   58U PubChem:   71340
DrugBank:   - ChEMBL:   CHEMBL423669
Molecular Formula:   C15H19N4O4S+ Mol. Weight:   351.11215 logP:   -0.5603
HBD:   2 HBA:   6
#Rotatable Bonds:   4 TPSA:   99.54
Covalent Mechanism
Reaction Name Residue Chain ID SASA pKa Warhead Name Warhead Structure
Beta-Lactam Addition CYS 354 A 11.01 13.88 Beta-Lactam
Binding Affinity
-