9TFB: PDGFRA-G680R mutant kinase domain

PDGFRA-G680R mutant kinase domain in complex with a 6,7-bis(2-methoxyethoxy)quinazoline-based compound (44). Determined by X-ray diffraction at 2.0 Å resolution. Released 15 Jul 2026.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,775
Mol. weight: 41.16 kDa
Ligands: A1JVS
Released: 15 Jul 2026

Explore 9TFB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9TFB contains 23 α-helices and 12 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 23 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	558-560	3
α-helix	562-563	2
α-helix	577-579	3
α-helix	581-582	2
α-helix	584-586	3
β-strand	587	1	1
α-helix	590-592	3
β-strand	593-601	9	1
β-strand	605-613	9	1
β-strand	621-629	9	1
α-helix	635-651	17
β-strand	657	1	2
β-strand	660-664	5	1
β-strand	671-675	5	1
α-helix	676-677	2
β-strand	681	1	2
α-helix	682-688	7
α-helix	690-693	4
α-helix	792-811	20
β-strand	814-815	2	3
α-helix	821-823	3
β-strand	824-828	5	2
β-strand	831-834	4	2
β-strand	841-842	2	3
α-helix	859-861	3
α-helix	864-869	6
α-helix	874-889	16
α-helix	893-894	2
α-helix	903-911	9
α-helix	915-918	4
α-helix	923-932	10
α-helix	937-939	3
α-helix	941-942	2
α-helix	943-951	9
α-helix	956-970	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Platelet-derived growth factor receptor alpha	A	protein	355	Homo sapiens	P16234 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9TFB_1 Platelet-derived growth factor receptor alpha (chains A)
GGRKQKPRYEIRWRVIESISPDGHEYIYVDPMQLPYDSRWEFPRDGLVLGRVLGSGAFGK
VVEGTAYGLSRSQPVMKVAVKMLKPTARSSEKQALMSELKIMTHLGPHLNIVNLLGACTK
SGPIYIITEYCFYRDLVNYLHKNRDSFLSHKKKSMLDSEVKNLLSDDNSEGLTLLDLLSF
TYQVARGMEFLASKNCVHRDLAARNVLLAQGKIVKICDFGLARDIMHDSNYVSKGSTFLP
VKWMAPESIFDNLYTTLSDVWSYGILLWEIFSLGGTPYPGMMVDSTFYNKIKSGYRMAKP
DHATSEVYEIMVKCWNSEPEKRPSFYHLSEIVENLLPGQYKKSYEKIHLDFLKSD

Ligands and cofactors

ID	Name	Formula	Copies
A1JVS	(1~{S})-1-[2-[4-[6,7-bis(2-methoxyethoxy)quinazolin-4-yl]piperazin-1-yl]pyrimid…	C30 H36 F N7 O4	1

Primary citation

Structure-based scaffold hopping reveals strategies to overcome oncogenic KIT and PDGFRA mutation-driven drug-resistance in GIST. Schulz, T., Beerbaum, M., Scrima, A. et al. Nat Commun (2026) 17. DOI 10.1038/s41467-026-76340-7 · PubMed

Other PDB entries of the same protein (UniProt P16234 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5GRN 1.77 Å, Crystal structure of PDGFRA in Complex with WQ-C-159
8PQJ 1.82 Å, PDGFRA wild-type kinase domain
6A32 1.87 Å, Crystal structure of PDGFRA kinase domain mutant T674I
6JOL 1.9 Å, Crystal structure of PDGFRA in complex with imatinib by co-crystallization
8PQK 2.0 Å, APO crystal structure of PDGFRA-T674I kinase domain
5K5X 2.17 Å, Crystal structure of human PDGFRA
9GZH 2.2 Å, PDGFRA-T674I in complex with covalent ponatinib derivative 19
9TF9 2.2 Å, PDGFRA-G680R mutant kinase domain in complex with avapritinib
9TFA 2.2 Å, PDGFRA-G680R mutant kinase domain in complex with a 6,7-dimethoxyquinazoline-based…
9TFC 2.3 Å, PDGFRA-G680R mutant kinase domain in complex with a 7-methoxyquinazolin-6-ol-based…
8PQH 2.5 Å, PDGFRA T674I mutant kinase domain in complex with avapritinib
6JOJ 2.6 Å, Crystal structure of PDGFRA T674I in complex with crenolanib by soaking

Browse structure collections

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