PDBsum entry 3nk8

Hydrolase

PDB id: 3nk8

Contents

Protein chain

223 a.a. *

Ligands

DMS ×4

JKZ

Metals

_CA

Waters ×408

* Residue conservation analysis

PDB id:

3nk8

Name:

Hydrolase

Title:

Trypsin in complex with fluorine-containing fragment

Structure:

Cationic trypsin. Chain: a. Synonym: beta-trypsin, alpha-trypsin chain 1, alpha-trypsin chain 2. Ec: 3.4.21.4

Source:

Bos taurus. Bovine. Organism_taxid: 9913

Resolution:

1.15Å R-factor: 0.123 R-free: 0.143

Authors:

N.Schiering,A.Vulpetti,C.Dalvit

Key ref:

A.Vulpetti et al. (2010). Combined use of computational chemistry, NMR screening, and X-ray crystallography for identification and characterization of fluorophilic protein environments. Proteins, 78, 3281-3291. PubMed id: 20886466

Date:

18-Jun-10 Release date: 10-Nov-10

Protein chain

P00760  (TRY1_BOVIN) -  Serine protease 1 from Bos taurus

Seq: 246 a.a.

Struc: 223 a.a.

Enzyme reactions

• Enzyme class: E.C.3.4.21.4 - trypsin.
• Reaction: Preferential cleavage: Arg-|-Xaa, Lys-|-Xaa.

Proteins 78:3281-3291 (2010)

PubMed id: 20886466

Combined use of computational chemistry, NMR screening, and X-ray crystallography for identification and characterization of fluorophilic protein environments.

A.Vulpetti, N.Schiering, C.Dalvit.

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.