9TF9 | pdb_00009tf9

PDGFRA-G680R mutant kinase domain in complex with avapritinib

• PDB DOI: https://doi.org/10.2210/pdb9TF9/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2025-11-27 Released: 2026-07-15 
• Deposition Author(s): Scrima, A., Mueller, M.P., Rauh, D.
• Funding Organization(s): German Research Foundation (DFG), European Regional Development Fund, German Federal Ministry for Education and Research, Other private, Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Structure-based Scaffold Hopping Reveals Strategies to Overcome Oncogenic KIT and PDGFRA Mutation-Driven Drug-Resistance in GIST

Schulz, T., Beerbaum, M., Scrima, A., Jantzen, H., Teuber, A., Muehlenberg, T., Garcia-Fossa, F., Weisner, J., Mueller, M.P., Sievers, S., Bauer, S., Rauh, D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 41.08 kDa 
• Atom Count: 2,638 
• Modeled Residue Count: 325 
• Deposited Residue Count: 355 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Platelet-derived growth factor receptor alpha	A	355	Homo sapiens	Mutation(s): 1  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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9JI (Subject of Investigation/LOI)	B [auth A]	Avapritinib C26 H27 F N10 DWYRIWUZIJHQKQ-SANMLTNESA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.62	α = 90
b = 72.91	β = 90
c = 102.07	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-07-15 
Deposition Author(s): Scrima, A., Mueller, M.P., Rauh, D.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	RA 1055/3-2
European Regional Development Fund	European Union	EFRE-800400
German Federal Ministry for Education and Research	Germany	InCa (01ZX2201B)
Other private		Ex-2021-0033
Other government		NW21-062C
Other private		MERCUR
Other private		Deutsche Krebshilfe (TACTIC)

Revision History  

• Version 1.0: 2026-07-15
  Type: Initial release