The structure of p38 alpha in complex with a triazol inhibitor

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 

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Ligand Structure Quality Assessment 

This is version 2.0 of the entry. See complete history


In Silico Identification of a Novel Hinge-Binding Scaffold for Kinase Inhibitor Discovery.

Wang, Y.Sun, Y.Cao, R.Liu, D.Xie, Y.Li, L.Qi, X.Huang, N.

(2017) J Med Chem 60: 8552-8564

  • DOI: https://doi.org/10.1021/acs.jmedchem.7b01075
  • Primary Citation of Related Structures:  
    5XYX, 5XYY, 5XYZ

  • PubMed Abstract: 

    To explore novel kinase hinge-binding scaffolds, we carried out structure-based virtual screening against p38α MAPK as a model system. With the assistance of developed kinase-specific structural filters, we identify a novel lead compound that selectively inhibits a panel of kinases with threonine as the gatekeeper residue, including BTK and LCK. These kinases play important roles in lymphocyte activation, which encouraged us to design novel kinase inhibitors as drug candidates for ameliorating inflammatory diseases and cancers. Therefore, we chemically modified our substituted triazole-class lead compound to improve the binding affinity and selectivity via a "minimal decoration" strategy, which resulted in potent and selective kinase inhibitors against LCK (18 nM) and BTK (8 nM). Subsequent crystallographic experiments validated our design. These rationally designed compounds exhibit potent on-target inhibition against BTK in B cells or LCK in T cells, respectively. Our work demonstrates that structure-based virtual screening can be applied to facilitate the development of novel chemical entities in crowded chemical space in the field of kinase inhibitor discovery.

  • Organizational Affiliation

    National Institute of Biological Sciences, Beijing , No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 14380Homo 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
P0F (Subject of Investigation/LOI)
Query on P0F

Download Ideal Coordinates CCD File 
B [auth A]3-(5-{[(2-chloro-6-fluorophenyl)methyl]amino}-4H-1,2,4-triazol-3-yl)phenol
C15 H12 Cl F N4 O
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.94α = 90
b = 86.6β = 90
c = 124.68γ = 90
Software Package:
Software NamePurpose
iMOSFLMdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-17
    Type: Initial release
  • Version 1.1: 2018-05-23
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description
  • Version 2.0: 2024-04-10
    Type: Coordinate replacement
    Reason: Model completeness
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Other, Refinement description, Source and taxonomy, Structure summary