6JOK

Crystal structure of PDGFRA in complex with sunitinib by soaking


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
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of PDGFRA in complex with sunitinib by soaking

Liang, L.Yan, X.E.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Platelet-derived growth factor receptor alpha356Homo sapiensMutation(s): 0 
Gene Names: PDGFRAPDGFR2RHEPDGFRA
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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16234
Sequence Annotations
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding 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 = 102.611α = 90
b = 102.611β = 90
c = 111.301γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina--

Revision History  (Full details and data files)

  • 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