Research workbench
Crystal structure of pdgfra in complex with imatinib by co- crystallization
Analyse Crystal structure of pdgfra in complex with imatinib by co- crystallization in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JOL
- Type
- protein
- Length
- 279 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Platelet-derived growth factor receptor alpha
- EC
- 2.7.10.1
- UniProt
- P16234
- Ligands
- STI
- Pockets
- 1 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Platelet-derived growth factor receptor alpha (EC 2.7.10.1) | protein | 279 | 39% helix, 19% strand | P16234 |
Ligands and binding sites
- STI · 4-(4-methyl-piperazin-1-ylmethyl)-N-[4-methyl-3-(4-pyridin-3-yl-pyrimidin-2-ylamino)-phenyl]-benzamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 572 | 0.74 | 0.81 | 60 | STI |
Compared structures
- 6JOL · Crystal structure of PDGFRA in complex with imatinib by co-crystallization · the same entry in another collection · chain A against A, TM-score 1.00
- P16234 · AlphaFold monomer V2.0 prediction for platelet-derived growth factor receptor alpha… · a predicted model of the same protein · chain A against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P16234
- Elsewhere: RCSB PDB 6JOL · PDBe 6JOL · UniProt P16234
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