P38 alpha kinase complexed with a pyrazolo-pyrimidine based inhibitor

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.319 
  • R-Value Work: 0.225 

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This is version 1.2 of the entry. See complete history


Pyrazolo-Pyrimidines: A Novel Heterocyclic Scaffold for Potent and Selective P38 Alpha Inhibitors.

Das, J.Moquin, R.V.Pitt, S.Zhang, R.Shen, D.R.Mcintyre, K.W.Gillooly, K.Doweyko, A.M.Sack, J.S.Zhang, H.Kiefer, S.E.Kish, K.Mckinnon, M.Barrish, J.C.Dodd, J.H.Schieven, G.L.Leftheris, K.

(2008) Bioorg Med Chem Lett 18: 2652

  • DOI: https://doi.org/10.1016/j.bmcl.2008.03.019
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The synthesis and structure-activity relationships (SAR) of p38 alpha MAP kinase inhibitors based on a pyrazolo-pyrimidine scaffold are described. These studies led to the identification of compound 2x as a potent and selective inhibitor of p38 alpha MAP kinase with excellent cellular potency toward the inhibition of TNFalpha production. Compound 2x was highly efficacious in vivo in inhibiting TNFalpha production in an acute murine model of TNFalpha production. X-ray co-crystallography of a pyrazolo-pyrimidine analog 2b bound to unphosphorylated p38 alpha is also disclosed.

  • Organizational Affiliation

    Bristol-Myers Squibb Research and Development, PO Box 4000, Princeton, NJ 08543-4000, USA. jagabandhu.das@bms.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 14366Homo 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 N4D

Download Ideal Coordinates CCD File 
B [auth A]N,4-dimethyl-3-[(1-phenyl-1H-pyrazolo[3,4-d]pyrimidin-4-yl)amino]benzamide
C20 H18 N6 O
Binding Affinity Annotations 
IDSourceBinding Affinity
N4D PDBBind:  3L8X Kd: 10 (nM) from 1 assay(s)
BindingDB:  3L8X IC50: 10 (nM) from 1 assay(s)
Binding MOAD:  3L8X IC50: 10 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.319 
  • R-Value Work: 0.225 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.392α = 90
b = 71.148β = 90
c = 73.12γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2010-03-02 
  • Deposition Author(s): Sack, J.S.
  • This entry supersedes: 3CG2

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2020-09-02
    Changes: Derived calculations, Structure summary