4C3F

Structure of Lck in complex with a compound discovered by Virtual Fragment Linking


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Efficient search of chemical space: navigating from fragments to structurally diverse chemotypes.

Wassermann, A.M.Kutchukian, P.S.Lounkine, E.Luethi, T.Hamon, J.Bocker, M.T.Malik, H.A.Cowan-Jacob, S.W.Glick, M.

(2013) J. Med. Chem. 56: 8879-8891

  • DOI: 10.1021/jm401309q

  • PubMed Abstract: 
  • We introduce a novel strategy to sample bioactive chemical space, which follows-up on hits from fragment campaigns without the need for a crystal structure. Our results strongly suggest that screening a few hundred or thousand fragments can substanti ...

    We introduce a novel strategy to sample bioactive chemical space, which follows-up on hits from fragment campaigns without the need for a crystal structure. Our results strongly suggest that screening a few hundred or thousand fragments can substantially improve the selection of small-molecule screening subsets. By combining fragment-based screening with virtual fragment linking and HTS fingerprints, we have developed an effective strategy not only to expand from low-affinity hits to potent compounds but also to hop in chemical space to substantially novel chemotypes. In benchmark calculations, our approach accessed subsets of compounds that were substantially enriched in chemically diverse hit compounds for various activity classes. Overall, half of the hits in the screening collection were found by screening only 10% of the library. Furthermore, a prospective application led to the discovery of two structurally novel histone deacetylase 4 inhibitors.


    Organizational Affiliation

    Novartis Institutes for Biomedical Research Inc. , 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TYROSINE-PROTEIN KINASE LCK
A
267Homo sapiensMutation(s): 1 
Gene Names: LCK
EC: 2.7.10.2
Find proteins for P06239 (Homo sapiens)
Go to Gene View: LCK
Go to UniProtKB:  P06239
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7KW
Query on 7KW

Download SDF File 
Download CCD File 
A
N-phenyl-4-(5-phenyl-1H-pyrazol-4-yl)pyrimidin-2-amine
C19 H15 N5
GHIDSWLDHRXNQM-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.177 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 58.088α = 90.00
b = 44.596β = 90.00
c = 120.254γ = 90.00
Software Package:
Software NamePurpose
REFMACphasing
XDSdata reduction
REFMACrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-23
    Type: Initial release
  • Version 1.1: 2014-01-15
    Type: Database references
  • Version 1.2: 2016-12-14
    Type: Data collection, Other
  • Version 1.3: 2018-04-04
    Type: Data collection
  • Version 1.4: 2019-02-27
    Type: Data collection, Database references, Experimental preparation