3ROC

Crystal structure of human p38 alpha complexed with a pyrimidinone compound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.239 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

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: 10.1016/j.bmcl.2011.05.006
  • Structures With Same Primary Citation

  • 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 ...

    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



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mitogen-activated protein kinase 14
A
360Homo sapiensMutation(s): 0 
Gene Names: CSBPCSBP1CSBP2CSPB1MAPK14MXI2THP-1SAPK2A
EC: 2.7.11.24
Find proteins for Q16539 (Homo sapiens)
Go to UniProtKB:  Q16539
NIH Common Fund Data Resources
PHAROS  Q16539
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
29A
Query on 29A

Download CCD File 
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
XIPYKUQAZQIESI-UHFFFAOYSA-N
 Ligand Interaction
29B
Query on 29B

Download CCD File 
A
4-[4-(4-fluorophenyl)-1H-pyrazol-3-yl]pyridine
C14 H10 F N3
UCYCFYFNBWRJIL-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
29AIC50:  17   nM  BindingDB
29AIC50:  12   nM  BindingDB
29AKi:  193   nM  BindingDB
29AKi :  6.400000095367432   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
X-PLORrefinement
HKL-2000data reduction
HKL-2000data scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2011-04-25 
  • Released Date: 2011-06-15 
  • Deposition Author(s): Shieh, H.-S., Xing, L.

Revision History 

  • Version 1.0: 2011-06-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance