Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 71.27 kDa 
• Atom Count: 4319 
• Modelled Residue Count: 549 
• Deposited Residue Count: 618 
• Unique protein chains: 1

4F63

Crystal structure of Human Fibroblast Growth Factor Receptor 1 Kinase domain in complex with compound 1

• PDB DOI: 10.2210/pdb4F63/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2012-05-14 Released: 2012-06-06 
• Deposition Author(s): Norman, R.A., Breed, J., Ogg, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.287 
• R-Value Work: 0.229 
• R-Value Observed: 0.232 

Literature

Protein-Ligand Crystal Structures Can Guide the Design of Selective Inhibitors of the FGFR Tyrosine Kinase.

Norman, R.A., Schott, A.K., Andrews, D.M., Breed, J., Foote, K.M., Garner, A.P., Ogg, D., Orme, J.P., Pink, J.H., Roberts, K., Rudge, D.A., Thomas, A.P., Leach, A.G.

(2012) J Med Chem 55: 5003-5012

• PubMed: 22612866 
• DOI: 10.1021/jm3004043
• Primary Citation of Related Structures:  
  4F63, 4F64, 4F65


• PubMed Abstract: 
  

The design of compounds that selectively inhibit a single kinase is a significant challenge, particularly for compounds that bind to the ATP site. We describe here how protein-ligand crystal structure information was able both to rationalize observed selectivity and to guide the design of more selective compounds. Inhibition data from enzyme and cellular screens and the crystal structures of a range of ligands tested during the process of identifying selective inhibitors of FGFR provide a step-by-step illustration of the process. Steric effects were exploited by increasing the size of ligands in specific regions in such a way as to be tolerated in the primary target and not in other related kinases. Kinases are an excellent target class to exploit such approaches because of the conserved fold and small side chain mobility of the active form.

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Organizational Affiliation: 

AstraZeneca Pharmaceuticals , Mereside, Alderley Park, Macclesfield, SK10 4TG, U.K.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fibroblast growth factor receptor 1	A, B	309	Homo sapiens	Mutation(s): 2  Gene Names: FGFR1, BFGFR, CEK, FGFBR, FLG, FLT2, HBGFR EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P11362 (Homo sapiens) Explore P11362  Go to UniProtKB:  P11362
PHAROS:  P11362 GTEx:  ENSG00000077782

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0S7	C [auth A], F [auth B]	5-bromo-N~4~-(3-methyl-1H-pyrazol-5-yl)-N~2~-[2-(pyridin-3-yl)ethyl]pyrimidine-2,4-diamine C15 H16 Br N7 UOHJGIQDKUHCQV-UHFFFAOYSA-N
EDO	D [auth A], E [auth A], G [auth B], H [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
0S7	PDBBind:  4F63	IC50: 500 (nM) from 1 assay(s)
	BindingDB:  4F63	IC50: min: 501.19, max: 2511.89 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.287 
• R-Value Work: 0.229 
• R-Value Observed: 0.232 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 208.306	α = 90
b = 57.477	β = 107.42
c = 65.452	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
AMoRE	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-05-14 
• Released Date: 2012-06-06 
Deposition Author(s): Norman, R.A., Breed, J., Ogg, D.

Revision History  

• Version 1.0: 2012-06-06
  Type: Initial release
  
• Version 1.1: 2012-06-27
  Changes: Database references