9GZH: PDGFRA-T674I

PDGFRA-T674I in complex with covalent ponatinib derivative 19. Determined by X-ray diffraction at 2.2 Å resolution. Released 12 Feb 2025.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,284
Mol. weight: 40.93 kDa
Ligands: A1IRC
Released: 12 Feb 2025

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

Secondary structure: helices and β-sheets

9GZH contains 17 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: 17 helices, 12 β-strands

Element	Residues	Length	Sheet
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	682-689	8
α-helix	792-811	20
α-helix	821-823	3
β-strand	824-827	4	2
β-strand	831-834	4	2
α-helix	838-840	3
β-strand	850-852	3	3
β-strand	855-857	3	3
α-helix	859-861	3
α-helix	864-869	6
α-helix	874-889	16
α-helix	893-894	2
α-helix	903-910	8
α-helix	915-918	4
α-helix	923-932	10
α-helix	937-939	3
α-helix	941-942	2
α-helix	943-953	11

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

>9GZH_1 Platelet-derived growth factor receptor alpha (chains A)
GPGKQKPRYEIRWRVIESISPDGHEYIYVDPMQLPYDSRWEFPRDGLVLGRVLGSGAFGK
VVEGTAYGLSRSQPVMKVAVKMLKPTARSSEKQALMSELKIMTHLGPHLNIVNLLGACTK
SGPIYIIIEYCFYGDLVNYLHKNRDSFLSHKKKSMLDSEVKNLLSDDNSEGLTLLDLLSF
TYQVARGMEFLASKNCVHRDLAARNVLLAQGKIVKICDFGLARDIMHDSNYVSKGSTFLP
VKWMAPESIFDNLYTTLSDVWSYGILLWEIFSLGGTPYPGMMVDSTFYNKIKSGYRMAKP
DHATSEVYEIMVKCWNSEPEKRPSFYHLSEIVENLLPGQYKKSYEKIHLDFLKSD

Ligands and cofactors

ID	Name	Formula	Copies
A1IRC	3-(2-imidazo[1,2-b]pyridazin-3-ylethynyl)-4-methyl-~{N}-[4-(propanoylamino)-3-(…	C26 H20 F3 N5 O2	1

Primary citation

Design, Synthesis, and SAR of Covalent KIT and PDGFRA Inhibitors─Exploring Their Potential in Targeting GIST. Schulz, T., Gontla, R., Teuber, A. et al. J Med Chem (2025) 68:3238-3259. DOI 10.1021/acs.jmedchem.4c02472 · 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
9TFB 2.0 Å, PDGFRA-G680R mutant kinase domain in complex with a 6,7-bis(2-methoxyethoxy)quinazoline-b…
5K5X 2.17 Å, Crystal structure of human PDGFRA
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

About this viewer

MolViewer shows 9GZH directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.