PDB Entry (4a52) |
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PDB ID: 4a52 | Resolution: - | Exp. Method: SOLUTION NMR |
PMID: 22579252 | DOI: 10.1016/J.STR.2012.03.015 | |
Protein |
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Protein Name: Putative L,D-transpeptidase YkuD | |
Uniprot ID/ACC: O34816 (YKUD_BACSU) | Organism: Bacillus subtilis (strain 168) |
Gene Symbol: ykuD | Gene ID: 939216 |
Protein Class: TRANSFERASE |
Ligand |
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Ligand Name: Imipenem | ||
Canonical SMILES: C[C@@H](O)[C@@H]1[C@H]2CC(SCCNC=N)=C(N2C1=O)C(O)=O | ||
Standard InChI: InChI=1S/C12H17N3O4S/c1-6(16)9-7-4-8(20-3-2-14-5-13)10(12(18)19)15(7)11(9)17/h5-7,9,16H,2-4H2,1H3,(H2,13,14)(H,18,19)/t6-,7-,9-/m1/s1 | ||
HET Code: IM2 | PubChem: 104838 | |
DrugBank: DB01598 | ChEMBL: CHEMBL148 | |
Molecular Formula: C12H17N3O4S | Mol. Weight: 299.09396 | logP: -0.17603 |
HBD: 4 | HBA: 5 | |
#Rotatable Bonds: 7 | TPSA: 113.72 |
Covalent Mechanism |
Reaction Name | Residue | Chain ID | SASA | pKa | Warhead Name | Warhead Structure |
Beta-Lactam Addition | CYS 142 | A | 34.22 | 10.97 | Beta-Lactam |
Binding Affinity |
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- |