PDB Entry (5dvp) |
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PDB ID: 5dvp | Resolution: 2.18 Å | Exp. Method: X-RAY DIFFRACTION |
PMID: 27820797 | DOI: 10.1038/nchembio.2237 | |
Protein |
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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 |
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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 |
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