Research workbench
Crystal structure of the catalytic domain of C-met kinase in complex with arq 197
Analyse Crystal structure of the catalytic domain of C-met kinase in complex with arq… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RHK
- Type
- protein
- Length
- 597 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
- M97
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hepatocyte growth factor receptor (EC 2.7.10.1) | protein | 298 | 36% helix, 16% strand | P08581 |
| B | Hepatocyte growth factor receptor (EC 2.7.10.1) | protein | 299 | 40% helix, 17% strand | P08581 |
Ligands and binding sites
- M97 · 1-[(3R,4R)-4-(1H-indol-3-yl)-2,5-dioxopyrrolidin-3-yl]pyrrolo[3,2,1-ij]quinolinium · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 317 | 0.71 | 0.84 | 37 | M97 |
| 2 | 426 | 0.70 | 0.81 | 50 | empty |
| 3 | 311 | 0.70 | 0.83 | 34 | M97 |
| 4 | 375 | 0.69 | 0.82 | 39 | empty |
| 5 | 123 | 0.38 | 0.74 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 308 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3RHK · Crystal structure of the catalytic domain of c-Met kinase in complex with ARQ 197 · 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 3RHK · PDBe 3RHK · UniProt P08581
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