The structure of p38alpha in complex with an arylpyridazinone

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

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This is version 1.5 of the entry. See complete history


p38 MAP Kinase Inhibitors Part 6: 2-Arylpyridazin-3-ones as templates for inhibitor design.

Natarajan, S.R.Heller, S.T.Nam, K.Singh, S.B.Scapin, G.Patel, S.Fitzgerald, C.E.Thompson, J.E.O'Keefe, S.J.

(2006) Bioorg Med Chem Lett 16: 5809-5813

  • DOI: https://doi.org/10.1016/j.bmcl.2006.08.074
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    p38 inhibitors based on 3,4-dihydropyrido[4,3-d]pyrimidazin-2-one template were synthesized and their SAR explored. Benchmark compounds 30, 35, and 36 were found to be potent against the enzyme. Crystal structure of p38 in complex with 30 indicated a key pi-stacking interaction with the pendant tyrosine residue-35 in the glycine-rich loop.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 14366Homo sapiensMutation(s): 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
Binding Affinity Annotations 
IDSourceBinding Affinity
222 PDBBind:  2I0H IC50: 9 (nM) from 1 assay(s)
Binding MOAD:  2I0H IC50: 9 (nM) from 1 assay(s)
BindingDB:  2I0H IC50: 9 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.722α = 90
b = 88.225β = 90
c = 121.456γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
MAR345data collection
DENZOdata reduction
SCALEPACKdata 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: 2006-10-17
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.5: 2023-08-30
    Changes: Data collection, Refinement description