6JOI: PDGFRA T674I

Crystal structure of PDGFRA T674I in complex with crenolanib by co-crystallization. Determined by X-ray diffraction at 3.1 Å resolution. Released 25 Mar 2020.

Method: X-ray diffraction
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,410
Mol. weight: 43.47 kDa
Ligands: 6T2
Released: 25 Mar 2020

Explore 6JOI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6JOI contains 17 α-helices and 10 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, 10 β-strands

Element	Residues	Length	Sheet
α-helix	577-579	3
α-helix	581-583	3
β-strand	587	1	1
α-helix	590-592	3
β-strand	593-601	9	1
β-strand	606-613	8	1
β-strand	621-628	8	1
α-helix	635-651	17
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	824-826	3	2
β-strand	832-834	3	2
α-helix	859-861	3
α-helix	864	1
α-helix	865-869	5
α-helix	874-889	16
α-helix	893-894	2
α-helix	903-911	9
α-helix	923-932	10
α-helix	937-939	3
α-helix	941-942	2
α-helix	943-951	9
α-helix	956-971	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Platelet-derived growth factor receptor alpha	A	protein	375	Homo sapiens	P16234 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6JOI_1 Platelet-derived growth factor receptor alpha (chains A)
HHHHHHDYDIPTTENLYFQGAMDKQKPRYEIRWRVIESISPDGHEYIYVDPMQLPYDSRW
EFPRDGLVLGRVLGSGAFGKVVEGTAYGLSRSQPVMKVAVKMLKPTARSSEKQALMSELK
IMTHLGPHLNIVNLLGACTKSGPIYIIIEYCFYGDLVNYLHKNRDSFLSHKKKSMLDSEV
KNLLSDDNSEGLTLLDLLSFTYQVARGMEFLASKNCVHRDLAARNVLLAQGKIVKICDFG
LARDIMHDSNYVSKGSTFLPVKWMAPESIFDNLYTTLSDVWSYGILLWEIFSLGGTPYPG
MMVDSTFYNKIKSGYRMAKPDHATSEVYEIMVKCWNSEPEKRPSFYHLSEIVENLLPGQY
KKSYEKIHLDFLKSD

Ligands and cofactors

ID	Name	Formula	Copies
6T2	1-(2-{5-[(3-Methyloxetan-3-yl)methoxy]-1H-benzimidazol-1-yl}quinolin-8-yl)piper…	C26 H29 N5 O2	1

Primary citation

Crystal structure of PDGFRA T674I in complex with crenolanib by co-crystallization. Liang, L., Yan, X.E. To be published.

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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