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
  • Primary Citation of Related Structures:  
    3ROC

  • 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 ...

    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: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 14 A360Homo sapiensMutation(s): 0 
Gene Names: CSBP, CSBP1, CSBP2, CSPB1, MAPK14, MXI2, THP-1, SAPK2A
EC: 2.7.11.24
Find proteins for Q16539 (Homo sapiens)
Explore Q16539 
Go to UniProtKB:  Q16539
NIH Common Fund Data Resources
PHAROS:  Q16539
GTEx:  ENSG00000112062
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
29A
Query on 29A
Download Ideal Coordinates 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 Ideal Coordinates 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


View more in-depth experimental data

Entry History 

Deposition Data

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

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