p38 Kinase crystal structure in complex with small molecule inhibitor

Experimental Data Snapshot

  • Resolution: 2.21 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


Fragment-Based Lead Discovery Using X-Ray Crystallography

Hartshorn, M.J.Murray, C.W.Cleasby, A.Frederickson, M.Tickle, I.J.Jhoti, H.

(2005) J Med Chem 48: 403

  • DOI: https://doi.org/10.1021/jm0495778
  • Primary Citation of Related Structures:  
    1W7H, 1WAX, 1WAY, 1WBG, 1WBO, 1WBU, 1WCC

  • PubMed Abstract: 

    Fragment screening offers an alternative to traditional screening for discovering new leads in drug discovery programs. This paper describes a fragment screening methodology based on high throughput X-ray crystallography. The method is illustrated against five proteins (p38 MAP kinase, CDK2, thrombin, ribonuclease A, and PTP1B). The fragments identified have weak potency (>100 microM) but are efficient binders relative to their size and may therefore represent suitable starting points for evolution to good quality lead compounds. The examples illustrate that a range of molecular interactions (i.e., lipophilic, charge-charge, neutral hydrogen bonds) can drive fragment binding and also that fragments can induce protein movement. We believe that the method has great potential for the discovery of novel lead compounds against a range of targets, and the companion paper illustrates how lead compounds have been identified for p38 MAP kinase starting from fragments such as those described in this paper.

  • Organizational Affiliation

    Astex Technology, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, United Kingdom.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MITOGEN-ACTIVATED PROTEIN KINASE 14360Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q16539 (Homo sapiens)
Explore Q16539 
Go to UniProtKB:  Q16539
PHAROS:  Q16539
GTEx:  ENSG00000112062 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16539
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 3IP

Download Ideal Coordinates CCD File 
C12 H12 N2 O
Binding Affinity Annotations 
IDSourceBinding Affinity
3IP BindingDB:  1W7H IC50: min: 1.00e+5, max: 1.30e+6 (nM) from 2 assay(s)
PDBBind:  1W7H IC50: 1.00e+6 (nM) from 1 assay(s)
Binding MOAD:  1W7H IC50: 1.00e+6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.21 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.771α = 90
b = 87.101β = 90
c = 126.337γ = 90
Software Package:
Software NamePurpose
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-02-08
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-07-05
    Changes: Data collection
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Refinement description