Crystal Structure of Human p38alpha complexed with a pyrimidopyridazinone compound

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 

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This is version 1.3 of the entry. See complete history


Discovery of N-substituted pyridinones as potent and selective inhibitors of p38 kinase.

Selness, S.R.Devraj, R.V.Monahan, J.B.Boehm, T.L.Walker, J.K.Devadas, B.Durley, R.C.Kurumbail, R.Shieh, H.Xing, L.Hepperle, M.Rucker, P.V.Jerome, K.D.Benson, A.G.Marrufo, L.D.Madsen, H.M.Hitchcock, J.Owen, T.J.Christie, L.Promo, M.A.Hickory, B.S.Alvira, E.Naing, W.Blevis-Bal, R.

(2009) Bioorg Med Chem Lett 19: 5851-5856

  • DOI: https://doi.org/10.1016/j.bmcl.2009.08.082
  • Primary Citation of Related Structures:  
    3HP2, 3HP5

  • PubMed Abstract: 

    The identification and evolution of a series of potent and selective p38 inhibitors is described. p38 inhibitors based on a N-benzyl pyridinone high-throughput screening hit were prepared and their SAR explored. Their design was guided by ligand bound co-crystals of p38alpha. These efforts resulted in the identification of 12r and 19 as orally active inhibitors of p38 with significant efficacy in both acute and chronic models of inflammation.

  • Organizational Affiliation

    Department of Medicinal Chemistry, Pfizer Corporation, 700 Chesterfield Parkway West, Chesterfield, MO 63017, USA. shaun.r.selness@pfizer.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 14360Homo sapiensMutation(s): 0 
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 52P

Download Ideal Coordinates CCD File 
B [auth A]5-(2,6-dichlorophenyl)-2-[(2,4-difluorophenyl)sulfanyl]-6H-pyrimido[1,6-b]pyridazin-6-one
C19 H9 Cl2 F2 N3 O S
Query on I46

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
C14 H9 F2 N3
Binding Affinity Annotations 
IDSourceBinding Affinity
52P BindingDB:  3HP5 Kd: min: 2.8, max: 1.00e+4 (nM) from 3 assay(s)
IC50: min: 0.8, max: 5300 (nM) from 13 assay(s)
PDBBind:  3HP5 IC50: 70 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.045α = 90
b = 74.022β = 90
c = 76.697γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data 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: 2009-09-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references, Derived calculations