Research workbench
C-met in complex with osi ligand
Analyse C-met in complex with osi ligand in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KNB
- Type
- protein
- Length
- 1,047 residues
- Chains
- 4
- 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
- 1RU, GBL
- Pockets
- 16 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hepatocyte growth factor receptor (EC 2.7.10.1) | protein | 273 | 40% helix, 18% strand | P08581 |
| B | Hepatocyte growth factor receptor (EC 2.7.10.1) | protein | 256 | 41% helix, 16% strand | P08581 |
| C | Hepatocyte growth factor receptor (EC 2.7.10.1) | protein | 271 | 42% helix, 16% strand | P08581 |
| D | Hepatocyte growth factor receptor (EC 2.7.10.1) | protein | 247 | 40% helix, 17% strand | P08581 |
Ligands and binding sites
- 1RU · 7-[(1R)-1-(2,6-dichloro-3-fluorophenyl)ethoxy]-3-[1-(piperidin-4-yl)-1H-pyrazol-4-yl]furo[3,2-c]pyridin-6-amine · ligand · 4 copies · chains A, C, B, D
- GBL · Gamma-butyrolactone · ligand · 3 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1001 | 0.74 | 0.77 | 89 | empty |
| 2 | 302 | 0.71 | 0.84 | 44 | 1RU, GBL |
| 3 | 281 | 0.70 | 0.84 | 34 | 1RU |
| 4 | 337 | 0.70 | 0.83 | 41 | 1RU |
| 5 | 602 | 0.69 | 0.78 | 60 | GBL |
Interfaces
5 interfaces between chains.
- A–C · 494 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 210 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 190 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 154 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 115 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4KNB · C-Met in complex with OSI ligand · 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 4KNB · PDBe 4KNB · UniProt P08581
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