3FLY

P38 kinase crystal structure in complex with 6-(2,4-difluoro-phenoxy)-2-isopropylamino-8-methyl-8h-pyrido[2,3-d]pyrimidin-7-one

• PDB DOI: https://doi.org/10.2210/pdb3FLY/pdb

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


• Deposited: 2008-12-19 Released: 2009-12-22 
• Deposition Author(s): Kuglstatter, A., Ghate, M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.245 
• R-Value Work: 0.220 

Literature

The Discovery of Pamapimod, R1503 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: 43.1 kDa 
• Atom Count: 3,113 
• 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
FLY	B [auth A]	6-(2,4-difluorophenoxy)-8-methyl-2-[(1-methylethyl)amino]pyrido[2,3-d]pyrimidin-7(8H)-one C17 H16 F2 N4 O2 HAVJVJFXQRMACG-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
FLY	BindingDB:  3FLY	IC50: 4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.245 
• R-Value Work: 0.220 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.465	α = 90
b = 85.791	β = 90
c = 124.911	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: Version format compliance
• Version 1.2: 2019-07-24
  Changes: Data collection, Refinement description
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations