PDB Entry (6iyv) |
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PDB ID: 6iyv | Resolution: 1.5 Å | Exp. Method: X-RAY DIFFRACTION |
PMID: 30686533 | DOI: 10.1016/j.bbrc.2019.01.082 | |
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: Ertapenem | ||
Canonical SMILES: C[C@@H](O)[C@@H]1[C@H]2[C@@H](C)C(S[C@@H]3CN[C@@H](C3)C(=O)NC3=CC=CC(=C3)C(O)=O)=C(N2C1=O)C(O)=O | ||
Standard InChI: InChI=1S/C22H25N3O7S/c1-9-16-15(10(2)26)20(28)25(16)17(22(31)32)18(9)33-13-7-14(23-8-13)19(27)24-12-5-3-4-11(6-12)21(29)30/h3-6,9-10,13-16,23,26H,7-8H2,1-2H3,(H,24,27)(H,29,30)(H,31,32)/t9-,10-,13+,14+,15-,16-/m1/s1 | ||
HET Code: 2RG | PubChem: 150610 | |
DrugBank: DB00303 | ChEMBL: CHEMBL1359 | |
Molecular Formula: C22H25N3O7S | Mol. Weight: 475.14133 | logP: 0.9407 |
HBD: 5 | HBA: 7 | |
#Rotatable Bonds: 7 | TPSA: 156.27 |
Covalent Mechanism |
Reaction Name | Residue | Chain ID | SASA | pKa | Warhead Name | Warhead Structure |
Beta-Lactam Addition | CYS 354 | B | 22.43 | 13.52 | Beta-Lactam |
Binding Affinity |
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