MolNFT v1 · #62440 · protein
Structure of C-met with pyrimidone inhibitor 50
3EFK · Hepatocyte growth factor receptor: “Structure of C-met with pyrimidone inhibitor 50”. X-ray diffraction, 1 ligand (MT4), 4 pockets (best druggability 0.72). MolNFT v1 #62440 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3EFK
- Type
- protein
- Length
- 548 residues
- Chains
- 2
- 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
- MT4
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hepatocyte growth factor receptor (EC 2.7.10.1) | protein | 276 | 41% helix, 15% strand | P08581 |
| B | Hepatocyte growth factor receptor (EC 2.7.10.1) | protein | 272 | 42% helix, 15% strand | P08581 |
Ligands and binding sites
- MT4 · 5-{4-[(6,7-dimethoxyquinolin-4-yl)oxy]-3-fluorophenyl}-2-[(4-fluorophenyl)amino]-3-methylpyrimidin-4(3H)-one · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 452 | 0.72 | 0.81 | 48 | MT4 |
| 2 | 396 | 0.70 | 0.81 | 41 | MT4 |
| 3 | 72 | 0.43 | 0.80 | 21 | empty |
| 4 | 73 | 0.36 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 996 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3EFK · Structure of c-Met with pyrimidone inhibitor 50 · the same entry in another collection · chain A against A, TM-score 1.00
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 3EFK · PDBe 3EFK · UniProt P08581
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