3NKK
Trypsin in complex with fluorine containing fragment
Summary for 3NKK
| Entry DOI | 10.2210/pdb3nkk/pdb |
| Related | 3NK8 |
| Descriptor | Cationic trypsin, DIMETHYL SULFOXIDE, CALCIUM ION, ... (5 entities in total) |
| Functional Keywords | beta barrel, chymotrypsin, chymotrypsin double beta barrel, peptide hydrolase, calcium binding, pancreas-duodenum, hydrolase |
| Biological source | Bos taurus (Bovine) |
| Cellular location | Secreted, extracellular space: P00760 |
| Total number of polymer chains | 1 |
| Total formula weight | 23829.07 |
| Authors | Schiering, N.,Vulpetti, A.,Dalvit, C. (deposition date: 2010-06-20, release date: 2010-11-10, Last modification date: 2024-11-20) |
| Primary citation | Vulpetti, A.,Schiering, N.,Dalvit, C. Combined use of computational chemistry, NMR screening, and X-ray crystallography for identification and characterization of fluorophilic protein environments. Proteins, 78:3281-3291, 2010 Cited by PubMed Abstract: (19)F NMR screening of fluorinated fragments with different Local Environment of Fluorine, a.k.a. LEF library, is an experimental methodology which, beyond providing useful starting fragments for fragment-based drug discovery projects, offers, in combination with crystal and computational analysis, an approach for the identification of fluorophilic hot-spots in the proteins of interest. The application of this approach in the identification of fluorinated fragments binding to the serine protease trypsin, and the X-ray structures of the complexes are presented. The specific nature of the observed fluorine-protein interactions is discussed and compared with the interactions detected for other fluorinated ligands reported in the protein data bank. The presence of similar 3D arrangements of protein atoms at the fluorine sub-sites is identified with a newly developed tool. In this approach, protein sub-sites are extracted around each fluorine contained in the protein data bank and compared with the query of interest by using a pharmacophoric description. PubMed: 20886466DOI: 10.1002/prot.22836 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.12 Å) |
Structure validation
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