6JOK

Crystal structure of PDGFRA in complex with sunitinib by soaking

• PDB DOI: https://doi.org/10.2210/pdb6JOK/pdb

• Classification: ONCOPROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2019-03-22 Released: 2020-03-25 
• Deposition Author(s): Liang, L., Yan, X.E., Yun, C.H.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.80 Å
• R-Value Free: 0.282 
• R-Value Work: 0.257 
• R-Value Observed: 0.259 

Starting Model: experimental

Literature

Crystal structure of PDGFRA in complex with sunitinib by soaking

Liang, L., Yan, X.E.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 41.06 kDa 
• Atom Count: 2,731 
• Modelled Residue Count: 338 
• Deposited Residue Count: 356 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Platelet-derived growth factor receptor alpha	A	356	Homo sapiens	Mutation(s): 0  Gene Names: PDGFRA, PDGFR2, RHEPDGFRA EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P16234 (Homo sapiens) Explore P16234  Go to UniProtKB:  P16234
PHAROS:  P16234 GTEx:  ENSG00000134853

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B49	B [auth A]	N-[2-(diethylamino)ethyl]-5-[(Z)-(5-fluoro-2-oxo-1,2-dihydro-3H-indol-3-ylidene)methyl]-2,4-dimethyl-1H-pyrrole-3-carbo xamide C22 H27 F N4 O2 WINHZLLDWRZWRT-ATVHPVEESA-N
CL	C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
B49	BindingDB:  6JOK	Kd: 0.79 (nM) from 1 assay(s)
		IC50: min: 6.9, max: 130 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.80 Å
• R-Value Free: 0.282 
• R-Value Work: 0.257 
• R-Value Observed: 0.259 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.611	α = 90
b = 102.611	β = 90
c = 111.301	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-03-25 
Deposition Author(s): Liang, L., Yan, X.E., Yun, C.H.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	--

Revision History  

• Version 1.0: 2020-03-25
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary