7PVU

Crystal structure of p38alpha C162S in complex with CAS2094511-69-8, P 1 21 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.205 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Characterization of p38 alpha autophosphorylation inhibitors that target the non-canonical activation pathway.

Gonzalez, L.Diaz, L.Pous, J.Baginski, B.Duran-Corbera, A.Scarpa, M.Brun-Heath, I.Igea, A.Martin-Malpartida, P.Ruiz, L.Pallara, C.Esguerra, M.Colizzi, F.Mayor-Ruiz, C.Biondi, R.M.Soliva, R.Macias, M.J.Orozco, M.Nebreda, A.R.

(2023) Nat Commun 14: 3318-3318

  • DOI: https://doi.org/10.1038/s41467-023-39051-x
  • Primary Citation of Related Structures:  
    7PVU, 7Z6I, 7Z9T

  • PubMed Abstract: 

    p38α is a versatile protein kinase that can control numerous processes and plays important roles in the cellular responses to stress. Dysregulation of p38α signaling has been linked to several diseases including inflammation, immune disorders and cancer, suggesting that targeting p38α could be therapeutically beneficial. Over the last two decades, numerous p38α inhibitors have been developed, which showed promising effects in pre-clinical studies but results from clinical trials have been disappointing, fueling the interest in the generation of alternative mechanisms of p38α modulation. Here, we report the in silico identification of compounds that we refer to as non-canonical p38α inhibitors (NC-p38i). By combining biochemical and structural analyses, we show that NC-p38i efficiently inhibit p38α autophosphorylation but weakly affect the activity of the canonical pathway. Our results demonstrate how the structural plasticity of p38α can be leveraged to develop therapeutic opportunities targeting a subset of the functions regulated by this pathway.


  • Organizational Affiliation

    Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 14
A, B
359Mus musculusMutation(s): 0 
Gene Names: Mapk14Crk1Csbp1Csbp2
EC: 2.7.11.24
UniProt
Find proteins for P47811 (Mus musculus)
Explore P47811 
Go to UniProtKB:  P47811
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP47811
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8DI (Subject of Investigation/LOI)
Query on 8DI

Download Ideal Coordinates CCD File 
C [auth B]N-(2-cyclobutyl-1H-1,3-benzodiazol-5-yl)-2-fluorobenzene-1-sulfonamide
C17 H16 F N3 O2 S
RNCGESUAFOAOBJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.205 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.141α = 90
b = 68.072β = 94.78
c = 79.98γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Science, Innovation, and UniversitiesSpainPID2019-109521RB-100
La Caixa FoundationSpainBioMedTec VIII - Nebre

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-17
    Type: Initial release
  • Version 1.1: 2023-06-14
    Changes: Database references
  • Version 1.2: 2023-06-21
    Changes: Database references
  • Version 1.3: 2024-02-07
    Changes: Data collection, Refinement description