Research workbench
X-ray structure of pf-02341066 bound to the kinase domain of C-met
Analyse X-ray structure of pf-02341066 bound to the kinase domain of C-met in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WGJ
- Type
- protein
- Length
- 289 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hepatocyte growth factor receptor
- EC
- 2.7.10.1
- UniProt
- P08581
- Ligands
- VGH
- Pockets
- 2 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hepatocyte growth factor receptor (EC 2.7.10.1) | protein | 289 | 41% helix, 16% strand | P08581 |
Ligands and binding sites
- VGH · 3-[(1R)-1-(2,6-dichloro-3-fluorophenyl)ethoxy]-5-(1-piperidin-4-yl-1H-pyrazol-4-yl)pyridin-2-amine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 197 | 0.67 | 0.85 | 25 | VGH |
| 2 | 194 | 0.53 | 0.78 | 24 | empty |
Compared structures
- 2WGJ · X-ray Structure of PF-02341066 bound to the kinase domain of c-Met · the same entry in another collection · chain A against A, TM-score 1.00
- P08581 · AlphaFold monomer V2.0 prediction for hepatocyte growth factor receptor (P08581) · a predicted model of the same protein · chain A against A, TM-score 0.91
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 P08581
- Elsewhere: RCSB PDB 2WGJ · PDBe 2WGJ · UniProt P08581
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