3ROC

Crystal structure of human p38 alpha complexed with a pyrimidinone compound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.276 
  • R-Value Work: 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

  • 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: MAPK14 (CSBP, CSBP1, CSBP2, CSPB1, MXI2, SAPK2A)
EC: 2.7.11.24
Find proteins for Q16539 (Homo sapiens)
Go to Gene View: MAPK14
Go to UniProtKB:  Q16539
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
29A
Query on 29A

Download SDF File 
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 SDF File 
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 %)
29AKi: 193 nM (100) BINDINGDB
29AIC50: 12 - 17 nM (100) BINDINGDB
29AKi: 6.4 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.239 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 65.311α = 90.00
b = 74.609β = 90.00
c = 77.752γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data collection
X-PLORmodel building
X-PLORphasing
X-PLORrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Version format compliance