3RIN

p38 kinase crystal structure in complex with small molecule inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3RIN/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-04-14 Released: 2012-02-29 
• Deposition Author(s): Segarra, V., Eastwood, P., Roca, R., Fisher, M., Lamers, M.

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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

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

• PubMed: 21696951 
• 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.

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Organizational Affiliation: 

Almirall Research Center, Almirall S.A., Ctra. Laureà Miró 408, E-08980 St. Feliu de Llobregat, Barcelona, Spain. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 41.7 kDa 
• Atom Count: 2,939 
• Modelled Residue Count: 349 
• Deposited Residue Count: 360 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 14	A	360	Homo sapiens	Mutation(s): 0  Gene Names: CSBP, CSBP1, CSBP2, CSPB1, MAPK14, MXI2 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
I2O	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
ID	Source	Binding 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 = 45.11	α = 90
b = 86.62	β = 90
c = 123.48	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
CrystalClear	data reduction
CrystalClear	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-29 
Deposition Author(s): Segarra, V., Eastwood, P., Roca, R., Fisher, M., Lamers, M.

Revision History  

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