8PQI: PDGFRA T674I mutant kinase domain

PDGFRA T674I mutant kinase domain in complex with avapritinib derivative 9. Determined by X-ray diffraction at 2.6 Å resolution. Released 27 Dec 2023.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,406
Mol. weight: 40.86 kDa
Ligands: 9OO
Released: 27 Dec 2023

Explore 8PQI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8PQI contains 18 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: 18 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	577-579	3
α-helix	581-583	3
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	636-651	16
β-strand	657	1	2
β-strand	660-664	5	1
β-strand	671-675	5	1
β-strand	680-681	2	2
α-helix	682-688	7
α-helix	792-811	20
β-strand	814-815	2	3
β-strand	824-827	4	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	915-917	3
α-helix	923-932	10
α-helix	937-939	3
α-helix	941-942	2
α-helix	943-952	10
α-helix	956-968	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Platelet-derived growth factor receptor alpha	A	protein	352	Homo sapiens	P16234 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8PQI_1 Platelet-derived growth factor receptor alpha (chains A)
KQKPRYEIRWRVIESISPDGHEYIYVDPMQLPYDSRWEFPRDGLVLGRVLGSGAFGKVVE
GTAYGLSRSQPVMKVAVKMLKPTARSSEKQALMSELKIMTHLGPHLNIVNLLGACTKSGP
IYIIIEYCFYGDLVNYLHKNRDSFLSHKKKSMLDSEVKNLLSDDNSEGLTLLDLLSFTYQ
VARGMEFLASKNCVHRDLAARNVLLAQGKIVKICDFGLARDIMHDSNYVSKGSTFLPVKW
MAPESIFDNLYTTLSDVWSYGILLWEIFSLGGTPYPGMMVDSTFYNKIKSGYRMAKPDHA
TSEVYEIMVKCWNSEPEKRPSFYHLSEIVENLLPGQYKKSYEKIHLDFLKSD

Ligands and cofactors

ID	Name	Formula	Copies
9OO	(1~{S})-~{N}-ethyl-1-(4-fluorophenyl)-1-[2-[4-[6-(1-methylpyrazol-4-yl)pyrrolo[…	C28 H31 F N10	1

Water and common crystallization additives (PEG) are not listed.

Primary citation

Avapritinib-based SAR studies unveil a binding pocket in KIT and PDGFRA. Teuber, A., Schulz, T., Fletcher, B.S. et al. Nat Commun (2024) 15:63-63. DOI 10.1038/s41467-023-44376-8 · 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
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

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