Research workbench
Crystal structure of human Proto-oncogene tyrosine-protein kinase receptor Ret in complex with 4-amino-7-(1-methylcyclopropyl)-N-(5-methyl-1H-pyrazol-3-yl)pyrrolo[2,3-d]pyrimidine-5-carboxamide
Analyse Crystal structure of human Proto-oncogene tyrosine-protein kinase receptor Ret… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DUA
- Type
- protein
- Length
- 561 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.64
- Source
- Homo sapiens
- Molecule
- Proto-oncogene tyrosine-protein kinase receptor Ret
- EC
- 2.7.10.1
- UniProt
- P07949
- Ligands
- HJ0
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · resolution 1.64 · 2 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proto-oncogene tyrosine-protein kinase receptor Ret (EC 2.7.10.1) | protein | 287 | 39% helix, 21% strand | P07949 |
| B | Proto-oncogene tyrosine-protein kinase receptor Ret (EC 2.7.10.1) | protein | 274 | 45% helix, 19% strand | P07949 |
Ligands and binding sites
- HJ0 · 4-azanyl-7-(1-methylcyclopropyl)-~{N}-(5-methyl-1~{H}-pyrazol-3-yl)pyrrolo[2,3-d]pyrimidine-5-carboxamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 667 | 0.79 | 0.84 | 83 | HJ0 |
| 2 | 364 | 0.67 | 0.80 | 42 | HJ0 |
| 3 | 133 | 0.47 | 0.78 | 25 | empty |
| 4 | 132 | 0.40 | 0.74 | 18 | empty |
| 5 | 67 | 0.34 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1433 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7DUA · Crystal structure of human proto-oncogene tyrosine-protein kinase receptor ret in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- P07949 · AlphaFold monomer V2.0 prediction for proto-oncogene tyrosine-protein kinase receptor ret… · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P07949
- Elsewhere: RCSB PDB 7DUA · PDBe 7DUA · UniProt P07949
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