› 8pqh

X-ray diffraction
2.5Å resolution

PDGFRA T674I mutant kinase domain in complex with avapritinib

Released:
DOI: 10.2210/pdb8pqh/pdb
Model geometry
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PDB entry 8pqh coloured by chain, front view.
PDB entry 8pqh coloured by chain, side view.
PDB entry 8pqh coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Avapritinib-based SAR studies unveil a binding pocket in KIT and PDGFRA.
Teuber A, Schulz T, Fletcher BS, Gontla R, Mühlenberg T, Zischinsky ML, Niggenaber J, Weisner J, Kleinbölting SB, Lategahn J, Sievers S, Müller MP, Bauer S, Rauh D
OpenAccess logo Nat Commun 15 63 (2024)
PMID: 38167404

Function and Biology Details

Reaction catalysed: 
ATP + a [protein]-L-tyrosine = ADP + a [protein]-L-tyrosine phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-147663 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Platelet-derived growth factor receptor alpha Chain: A
Molecule details ›
Chain: A
Length: 352 amino acids
Theoretical weight: 40.23 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P16234 (Residues: 550-973; Coverage: 33%)
  • Best match: P16234-3 (Residues: 550-706)
Gene names: PDGFR2, PDGFRA, RHEPDGFRA
Sequence domains: Protein tyrosine and serine/threonine kinase

Ligands and Environments

2 bound ligands:
Ligand 9JI 1 x 9JI
Ligand PEG 1 x PEG
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SLS BEAMLINE X10SA
Spacegroup: P212121
Unit cell:
a: 52.27Å b: 73.26Å c: 102.59Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.22 0.218 0.249
Expression system: Spodoptera frugiperda

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Citations

1 review citation

Mechanistic insights and the clinical prospects of targeted therapies for glioblastoma: a comprehensive review.
Shen et al. (2024)
1 other article

2 mentions without citation

Impact of structural biology and the protein data bank on us fda new drug approvals of low molecular weight antineoplastic agents 2019-2023.
Burley et al. (2024)
1 more

PDB-REDO

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