MolNFT v1 · #63316 · protein
Human C-met kinase in complex with quinoxaline inhibitor
3F66 · Hepatocyte growth factor receptor: “Human C-met kinase in complex with quinoxaline inhibitor”. X-ray diffraction, 3 ligands (GBL, IHX, NA), 10 pockets (best druggability 0.69). MolNFT v1 #63316 on GenesisL1: 3D structure, binding…
- PDB
- 3F66
- Type
- protein
- Length
- 557 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
- GBL, IHX, NA
- Pockets
- 10 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hepatocyte growth factor receptor (EC 2.7.10.1) | protein | 288 | 43% helix, 16% strand | P08581 |
| B | Hepatocyte growth factor receptor (EC 2.7.10.1) | protein | 269 | 42% helix, 15% strand | P08581 |
Ligands and binding sites
- GBL · Gamma-butyrolactone · ligand · 5 copies · chains A, B
- IHX · 3-[3-(4-methylpiperazin-1-yl)-7-(trifluoromethyl)quinoxalin-5-yl]phenol · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 728 | 0.69 | 0.76 | 68 | GBL |
| 2 | 258 | 0.67 | 0.83 | 28 | IHX, GBL |
| 3 | 253 | 0.66 | 0.82 | 26 | IHX, GBL |
| 4 | 136 | 0.52 | 0.80 | 21 | empty |
| 5 | 142 | 0.51 | 0.80 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 841 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3F66 · Human c-Met Kinase in complex with quinoxaline inhibitor · 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 3F66 · PDBe 3F66 · UniProt P08581
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