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 

wwPDB Validation 3D Report Full Report


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

  • 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 com ...

    (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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cationic trypsinA223Bos taurusMutation(s): 0 
EC: 3.4.21.4
Find proteins for P00760 (Bos taurus)
Explore P00760 
Go to UniProtKB:  P00760
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JKZ
Query on JKZ

Download CCD File 
A
4-(trifluoromethyl)-1,5,6,7-tetrahydro-2H-cyclopenta[b]pyridin-2-one
C9 H8 F3 N O
GSJGKNLMGQIWJH-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
JKZKd :  1000000   nM  PDBBind
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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Entry History 

Deposition Data

Revision History 

  • 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