3FMH

P38 kinase crystal structure in complex with 6-(2,4-Difluoro-phenoxy)-8-methyl-2-((R)-1-methyl-2-tetrazol-2-yl-ethylamino)-8H-pyrido[2,3-d]pyrimidin-7-one

• PDB DOI: https://doi.org/10.2210/pdb3FMH/pdb

• Classification: SIGNALING PROTEIN, TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-12-22 Released: 2009-12-22 
• Deposition Author(s): Kuglstatter, A., Ghate, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.246 
• R-Value Work: 0.217 
• R-Value Observed: 0.218 

Starting Model: experimental

Literature

The Discovery of Pamapimod and R1487 as Orally Bioavailable and Highly Selective Inhibitors of p38 Map Kinase

Soth, M., Kuglstatter, A., Goldstein, D.

To be published.

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: 43.16 kDa 
• Atom Count: 3,076 
• Modelled Residue Count: 347 
• Deposited Residue Count: 372 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 14	A	372	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
533	B [auth A]	6-(2,4-difluorophenoxy)-8-methyl-2-{[(1R)-1-methyl-2-(2H-tetrazol-2-yl)ethyl]amino}pyrido[2,3-d]pyrimidin-7(8H)-one C18 H16 F2 N8 O2 WIGNNIARPGHXFO-SNVBAGLBSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
533	BindingDB:  3FMH	IC50: 11 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.246 
• R-Value Work: 0.217 
• R-Value Observed: 0.218 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.654	α = 90
b = 85.914	β = 90
c = 126.37	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CNS	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-22 
Deposition Author(s): Kuglstatter, A., Ghate, M.

Revision History  

• Version 1.0: 2009-12-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2019-07-24
  Changes: Data collection, Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description