8RHR
E.coli Peptide Deformylase with bound inhibitor BB4
Summary for 8RHR
| Entry DOI | 10.2210/pdb8rhr/pdb |
| Descriptor | Peptide deformylase, ZINC ION, 2-(5-bromo-1H-indol-3-yl)-N-hydroxyacetamide, ... (6 entities in total) |
| Functional Keywords | peptide deformylase (ec 3.5.1.88), inhibitor, hydrolase |
| Biological source | Escherichia coli |
| Total number of polymer chains | 1 |
| Total formula weight | 20135.51 |
| Authors | Kirschner, H.,Stoll, R.,Hofmann, E. (deposition date: 2023-12-16, release date: 2024-04-17, Last modification date: 2024-05-08) |
| Primary citation | Kirschner, H.,Heister, N.,Zouatom, M.,Zhou, T.,Hofmann, E.,Scherkenbeck, J.,Stoll, R. Toward More Selective Antibiotic Inhibitors: A Structural View of the Complexed Binding Pocket of E. coli Peptide Deformylase. J.Med.Chem., 67:6384-6396, 2024 Cited by PubMed Abstract: Peptide deformylase (PDF) is involved in bacterial protein maturation processes. Originating from the interest in a new antibiotic, tremendous effort was put into the refinement of PDF inhibitors (PDFIs) and their selectivity. We obtained a full NMR backbone assignment the emergent additional protein backbone resonances of ecPDF 1-147 in complex with 2-(5-bromo-1-indol-3-yl)--hydroxyacetamide (), a potential new structural scaffold for more selective PDFIs. We also determined the complex crystal structures of PDF (ecPDF fl) and . Our structure suggests an alternative ligand conformation within the protein, a possible starting point for further selectivity optimization. The orientation of the second ligand conformation in the crystal structure points toward a small region of the S1' pocket, which differs between bacterial PDFs and human PDF. Moreover, we analyzed the binding mode of via NMR TITAN line shape analysis, revealing an induced fit mechanism. PubMed: 38574272DOI: 10.1021/acs.jmedchem.3c02382 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.42 Å) |
Structure validation
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