MolNFT v1 · #62439 · protein
Structure of C-met with pyrimidone inhibitor 7
3EFJ · Hepatocyte growth factor receptor: “Structure of C-met with pyrimidone inhibitor 7”. X-ray diffraction, 1 ligand (MT3), 2 pockets (best druggability 0.75). MolNFT v1 #62439 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3EFJ
- Type
- protein
- Length
- 551 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
- MT3
- Pockets
- 2 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hepatocyte growth factor receptor (EC 2.7.10.1) | protein | 276 | 39% helix, 15% strand | P08581 |
| B | Hepatocyte growth factor receptor (EC 2.7.10.1) | protein | 275 | 40% helix, 16% strand | P08581 |
Ligands and binding sites
- MT3 · 2-benzyl-5-{4-[(6,7-dimethoxyquinolin-4-yl)oxy]-3-fluorophenyl}-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
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 | 499 | 0.75 | 0.83 | 48 | MT3 |
| 2 | 614 | 0.72 | 0.79 | 55 | MT3 |
Interfaces
1 interface between chains.
- A–B · 938 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3EFJ · Structure of c-Met with pyrimidone inhibitor 7 · 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 3EFJ · PDBe 3EFJ · UniProt P08581
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