Crystal structure of human p38 alpha complexed with a pyrimidinone compound

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.239 

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This is version 1.2 of the entry. See complete history


Substituted N-aryl-6-pyrimidinones: A new class of potent, selective, and orally active p38 MAP kinase inhibitors.

Devadas, B.Selness, S.R.Xing, L.Madsen, H.M.Marrufo, L.D.Shieh, H.Messing, D.M.Yang, J.Z.Morgan, H.M.Anderson, G.D.Webb, E.G.Zhang, J.Devraj, R.V.Monahan, J.B.

(2011) Bioorg Med Chem Lett 21: 3856-3860

  • DOI: https://doi.org/10.1016/j.bmcl.2011.05.006
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    A novel series of highly potent and selective p38 MAP kinase inhibitors was developed originating from a substituted N-aryl-6-pyrimidinone scaffold. SAR studies coupled with in vivo evaluations in rat arthritis model culminated in the identification of 10 with excellent oral efficacy. Compound 10 exhibited a significantly enhanced dissolution rate compared to 1, translating to a high oral bioavailability (>90%) in rat. In animal studies 10 inhibited LPS-stimulated production of tumor necrosis factor-α in a dose-dependent manner and demonstrated robust efficacy comparable to dexamethasone in a rat streptococcal cell wall-induced arthritis model.

  • Organizational Affiliation

    Department of Medicinal Chemistry, Pfizer Corporation, 700 Chesterfield Parkway West, Chesterfield, MO 63017, USA. balekudru.devadas@yahoo.com

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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 29A

Download Ideal Coordinates CCD File 
B [auth A]3-{5-chloro-4-[(2,4-difluorobenzyl)oxy]-6-oxopyrimidin-1(6H)-yl}-N-(2-hydroxyethyl)-4-methylbenzamide
C21 H18 Cl F2 N3 O4
Query on 29B

Download Ideal Coordinates CCD File 
C [auth A]4-[4-(4-fluorophenyl)-1H-pyrazol-3-yl]pyridine
C14 H10 F N3
Binding Affinity Annotations 
IDSourceBinding Affinity
29A BindingDB:  3ROC Ki: 193 (nM) from 1 assay(s)
IC50: min: 12, max: 17 (nM) from 2 assay(s)
PDBBind:  3ROC Ki: 6.4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.239 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.311α = 90
b = 74.609β = 90
c = 77.752γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
X-PLORmodel building
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-06-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations