5GRN

Crystal structure of PDGFRA in Complex with WQ-C-159

• PDB DOI: https://doi.org/10.2210/pdb5GRN/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2016-08-11 Released: 2017-08-16 
• Deposition Author(s): Yan, X.E., Yun, C.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 0.179 
• R-Value Work: 0.157 
• R-Value Observed: 0.158 

Starting Model: experimental

Literature

Crystal Structure of PDGFRA in Complex with WQ-C-159

Yan, X.E., Yun, C.H.

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: 41.28 kDa 
• Atom Count: 2,716 
• Modelled Residue Count: 286 
• 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
748	B [auth A]	N-[2-(dimethylamino)ethyl]-N-[[4-[[4-methyl-3-[(4-pyridin-3-ylpyrimidin-2-yl)amino]phenyl]carbamoyl]phenyl]methyl]pyridine-3-carboxamide C34 H34 N8 O2 NWVOHJOHQOHBMB-UHFFFAOYSA-N
CL	C [auth A], D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
748	BindingDB:  5GRN	IC50: 132 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 0.179 
• R-Value Work: 0.157 
• R-Value Observed: 0.158 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.776	α = 90
b = 49.372	β = 90
c = 108.696	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-08-16 
Deposition Author(s): Yan, X.E., Yun, C.H.

Revision History  

• Version 1.0: 2017-08-16
  Type: Initial release
  
• Version 1.1: 2017-10-04
  Changes: Data collection
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description