PDB Entry (6kgv)
PDB ID: 6kgv Resolution: 2.3 Å Exp. Method: X-RAY DIFFRACTION
PMID: 32086254 DOI: 10.1124/mol.119.118042
Protein
Protein Name: Penicillin-binding protein PbpB
Uniprot ID/ACC: L0T911 (PBPB_MYCTU) Organism: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Gene Symbol: pbpB Gene ID: 887949
Protein Class: TRANSFERASE
Ligand
Ligand Name:   Amoxicillin
Canonical SMILES:   CC1(C)S[C@@H]2[C@H](NC(=O)[C@H](N)c3ccc(O)cc3)C(=O)N2[C@H]1C(O)=O
Standard InChI:   InChI=1S/C16H19N3O5S/c1-16(2)11(15(23)24)19-13(22)10(14(19)25-16)18-12(21)9(17)7-3-5-8(20)6-4-7/h3-6,9-11,14,20H,17H2,1-2H3,(H,18,21)(H,23,24)/t9-,10-,11+,14-/m1/s1
HET Code:   AXL PubChem:   33613
DrugBank:   DB01060 ChEMBL:   CHEMBL1082
Molecular Formula:   C16H19N3O5S Mol. Weight:   365.10455 logP:   0.0237
HBD:   4 HBA:   6
#Rotatable Bonds:   4 TPSA:   132.96
Covalent Mechanism
Reaction Name Residue Chain ID SASA pKa Warhead Name Warhead Structure
Beta-Lactam Addition SER 386 A 15.32 - Beta-Lactam
Binding Affinity
-