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: 71.62 kDa 
• Atom Count: 4645 
• Modelled Residue Count: 566 
• Deposited Residue Count: 618 
• Unique protein chains: 1

4NKA

Crystal structure of human fibroblast growth factor receptor 1 kinase domain in complex with pyrazolaminopyrimidine 2

• PDB DOI: 10.2210/pdb4NKA/pdb

• Classification: transferase/transferase inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-11-12 Released: 2013-12-18 
• Deposition Author(s): Norman, R.A., Klein, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 0.228 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 

Literature

FGFR1 Kinase Inhibitors: Close Regioisomers Adopt Divergent Binding Modes and Display Distinct Biophysical Signatures.

Klein, T., Tucker, J., Holdgate, G.A., Norman, R.A., Breeze, A.L.

(2014) ACS Med Chem Lett 5: 166-171

• PubMed: 24900792 
• DOI: 10.1021/ml4004205
• Primary Citation of Related Structures:  
  4NK9, 4NKA, 4NKS


• PubMed Abstract: 
  

The binding of a ligand to its target protein is often accompanied by conformational changes of both the protein and the ligand. This is of particular interest, since structural rearrangements of the macromolecular target and the ligand influence the free energy change upon complex formation. In this study, we use X-ray crystallography, isothermal titration calorimetry, and surface-plasmon resonance biosensor analysis to investigate the binding of pyrazolylaminopyrimidine inhibitors to FGFR1 tyrosine kinase, an important anticancer target. Our results highlight that structurally close analogs of this inhibitor series interact with FGFR1 with different binding modes, which are a consequence of conformational changes in both the protein and the ligand as well as the bound water network. Together with the collected kinetic and thermodynamic data, we use the protein-ligand crystal structure information to rationalize the observed inhibitory potencies on a molecular level.

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Organizational Affiliation: 

Discovery Sciences, AstraZeneca R&D , Alderley Park, Macclesfield, Cheshire, 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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2K7	G [auth A], J [auth B]	N~4~-{3-[2-(3,4-dimethoxyphenyl)ethyl]-1H-pyrazol-5-yl}-N~2~-[(3-methyl-1,2-oxazol-5-yl)methyl]pyrimidine-2,4-diamine C22 H25 N7 O3 YLSKPWFLSHNDEO-UHFFFAOYSA-N
SO4	C [auth A], D [auth A], H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	E [auth A], F [auth A], I [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
2K7	Binding MOAD:  4NKA	Kd: 447 (nM) from 1 assay(s)
	PDBBind:  4NKA	Kd: 311.4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 0.228 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 208.83	α = 90
b = 57.36	β = 107.68
c = 65.73	γ = 90

Software Package:

Software Name	Purpose
GDA	data collection
AMoRE	phasing
BUSTER	refinement
XDS	data reduction
Aimless	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-11-12 
• Released Date: 2013-12-18 
Deposition Author(s): Norman, R.A., Klein, T.

Revision History  

• Version 1.0: 2013-12-18
  Type: Initial release
  
• Version 1.1: 2014-07-16
  Changes: Database references