Crystal structure of p38 alpha in complex with compound 75 (MCP33)

Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 

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This is version 1.2 of the entry. See complete history


Fast Iterative Synthetic Approach toward Identification of Novel Highly Selective p38 MAP Kinase Inhibitors.

Rohm, S.Berger, B.T.Schroder, M.Chaikuad, A.Winkel, R.Hekking, K.F.W.Benningshof, J.J.C.Muller, G.Tesch, R.Kudolo, M.Forster, M.Laufer, S.Knapp, S.

(2019) J Med Chem 62: 10757-10782

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b01227
  • Primary Citation of Related Structures:  
    6SFI, 6SFJ, 6SFK

  • PubMed Abstract: 

    p38 mitogen-activated protein kinases are key mediators of environmental stress response and are promising targets for treatment of inflammatory diseases and cancer. Numerous efforts have led to the discovery of several potent inhibitors; however, so far no highly selective type-II inhibitors have been reported. We previously identified VPC-00628 as a potent and selective type-II inhibitor of p38α/β with few off-targets. Here we analyzed the chemical building blocks of VPC-00628 that played a key role in achieving potency and selectivity through targeting an inactive state of the kinases induced by a unique folded P-loop conformation. Using a rapid, systematic combinatorial synthetic approach, we identified compound 93 ( SR-318 ) with excellent potency and selectivity for p38α/β, which potently inhibited the TNF-α release in whole blood. SR-318 therefore presents a potent and selective type-II inhibitor of p38α/β that can be used as a chemical probe for targeting this particular inactive state of these two p38 isoforms.

  • Organizational Affiliation

    Institute for Pharmaceutical Chemistry , Johann Wolfgang Goethe-University , Max-von-Laue-Str. 9 , D-60438 Frankfurt am Main , Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 14361Homo 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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LB5 (Subject of Investigation/LOI)
Query on LB5

Download Ideal Coordinates CCD File 
B [auth A]~{N}-[(2~{S})-1-azanyl-4-cyclohexyl-1-oxidanylidene-butan-2-yl]-2-[[[1-(2-methylphenyl)pyrazol-4-yl]carbonylamino]methyl]-1,3-thiazole-5-carboxamide
C26 H32 N6 O3 S
Experimental Data & Validation

Experimental Data

  • Resolution: 1.60 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.449α = 90
b = 71.289β = 90
c = 76.2γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-11
    Type: Initial release
  • Version 1.1: 2020-01-29
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description