PDB Entry (5dc2) |
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PDB ID: 5dc2 | Resolution: 2.18 Å | Exp. Method: X-RAY DIFFRACTION |
PMID: 28545389 | DOI: 10.1186/s12858-017-0082-4 | |
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: 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 | 11.84 | 13.88 | Beta-Lactam |
Binding Affinity |
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