3NK8

Trypsin in complex with fluorine-containing fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.143 
  • R-Value Work: 0.122 
  • R-Value Observed: 0.123 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

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

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

(2010) Proteins 78: 3281-3291

  • DOI: https://doi.org/10.1002/prot.22836
  • Primary Citation of Related Structures:  
    3NK8, 3NKK

  • 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.


  • Organizational Affiliation

    Global Chemistry Discovery, Novartis Institutes for Biomedical Research, CH-4002 Basel, Switzerland. anna.vulpetti@novartis.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cationic trypsin223Bos taurusMutation(s): 0 
EC: 3.4.21.4
UniProt
Find proteins for P00760 (Bos taurus)
Explore P00760 
Go to UniProtKB:  P00760
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00760
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.143 
  • R-Value Work: 0.122 
  • R-Value Observed: 0.123 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.72α = 90
b = 58.266β = 90
c = 66.77γ = 90
Software Package:
Software NamePurpose
MAR345data collection
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-11-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Refinement description