Crystal structure of p38 MAP kinase in complex with a dihydroquinazolinone inhibitor

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.217 

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This is version 1.5 of the entry. See complete history


Design and synthesis of potent, orally bioavailable dihydroquinazolinone inhibitors of p38 MAP kinase.

Stelmach, J.E.Liu, L.Patel, S.B.Pivnichny, J.V.Scapin, G.Singh, S.Hop, C.E.Wang, Z.Strauss, J.R.Cameron, P.M.Nichols, E.A.O'Keefe, S.J.O'Neill, E.A.Schmatz, D.M.Schwartz, C.D.Thompson, C.M.Zaller, D.M.Doherty, J.B.

(2003) Bioorg Med Chem Lett 13: 277-280

  • DOI: https://doi.org/10.1016/s0960-894x(02)00752-7
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The development of potent, orally bioavailable (in rat) and selective dihydroquinazolinone inhibitors of p38alpha MAP kinase is described. These analogues are hybrids of a pyridinylimidazole p38alpha inhibitor reported by Merck Research Laboratories and VX-745. Optimization of the C-5 phenyl and the C-7 piperidinyl substituents led to the identification of 15i which gave excellent suppression of TNF-alpha production in LPS-stimulated whole blood (IC(50)=10nM) and good oral exposure in rats (F=68%, AUCn PO=0.58 microM h).

  • Organizational Affiliation

    Department of Medicinal Chemistry, Merck Research Laboratories, PO Box 2000, Rahway, NJ 07065, USA. john_stelmach@merck.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 14366Homo sapiensMutation(s): 0 
EC: 2.7.1
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 DQO

Download Ideal Coordinates CCD File 
C24 H20 Cl2 F2 N4 O
Query on SO4

Download Ideal Coordinates CCD File 
O4 S
Binding Affinity Annotations 
IDSourceBinding Affinity
DQO BindingDB:  1M7Q IC50: min: 2.6, max: 67 (nM) from 5 assay(s)
PDBBind:  1M7Q IC50: 2.6 (nM) from 1 assay(s)
Binding MOAD:  1M7Q IC50: 2.6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.217 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.516α = 90
b = 87.163β = 90
c = 124.939γ = 90
Software Package:
Software NamePurpose
MAR345data collection
X-GENdata reduction
X-GENdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2002-12-11
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2018-01-24
    Changes: Structure summary
  • Version 1.5: 2024-02-14
    Changes: Data collection, Database references, Derived calculations, Refinement description