MolNFT v1 · #116517 · protein
Crystal structure of the tyrosine kinase domain of the hepatocyte growth factor receptor C-met in complex with altiratinib analog dp- 4157
5DG5: “Crystal structure of the tyrosine kinase domain of the hepatocyte growth factor receptor C-met in complex…”. X-ray diffraction, 1 ligand (5B4), 5 pockets (best druggability 0.76). MolNFT v1 #116517 on GenesisL1: 3D structure…
- PDB
- 5DG5
- Type
- protein
- Length
- 594 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
- 5B4
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hepatocyte growth factor receptor (EC 2.7.10.1) | protein | 297 | 38% helix, 18% strand | P08581 |
Ligands and binding sites
- 5B4 · N-(2,5-difluoro-4-{[2-(1-methyl-1H-pyrazol-4-yl)pyridin-4-yl]oxy}phenyl)-N'-(4-fluorophenyl)cyclopropane-1,1-dicarboxam ide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 620 | 0.76 | 0.82 | 63 | 5B4 |
| 2 | 642 | 0.75 | 0.81 | 64 | 5B4 |
| 3 | 352 | 0.60 | 0.77 | 39 | empty |
| 4 | 137 | 0.41 | 0.75 | 22 | empty |
| 5 | 129 | 0.40 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 186 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5DG5 · Crystal structure of the tyrosine kinase domain of the hepatocyte growth factor receptor… · 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 5DG5 · PDBe 5DG5 · UniProt P08581
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