3RIN

p38 kinase crystal structure in complex with small molecule inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.265 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Indolin-2-one p38(alpha) inhibitors I: design, profiling and crystallographic binding mode.

Eastwood, P.Gonzalez, J.Gomez, E.Vidal, B.Caturla, F.Roca, R.Balague, C.Orellana, A.Dominguez, M.

(2011) Bioorg Med Chem Lett 21: 4130-4133

  • DOI: https://doi.org/10.1016/j.bmcl.2011.05.114
  • Primary Citation of Related Structures:  
    3RIN

  • PubMed Abstract: 

    The use of structure-based design and molecular modeling led to the discovery of indolin-2-one derivatives as potent and selective p38α inhibitors. The predicted binding mode was confirmed by X-ray crystallography.


  • Organizational Affiliation

    Almirall Research Center, Almirall S.A., Ctra. Laureà Miró 408, E-08980 St. Feliu de Llobregat, Barcelona, Spain. paul.eastwood@almirall.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 14360Homo sapiensMutation(s): 0 
Gene Names: CSBPCSBP1CSBP2CSPB1MAPK14MXI2
EC: 2.7.11.24
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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
I2O
Query on I2O

Download Ideal Coordinates CCD File 
B [auth A]N-cyclopropyl-4-methyl-3-(2'-oxo-1',2'-dihydrospiro[cyclopentane-1,3'-indol]-6'-yl)benzamide
C23 H24 N2 O2
WMXJYEDCJIDCNY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
I2O PDBBind:  3RIN IC50: 1.3 (nM) from 1 assay(s)
BindingDB:  3RIN IC50: 1.3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.265 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.11α = 90
b = 86.62β = 90
c = 123.48γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-29
    Type: Initial release
  • Version 1.1: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description