Research workbench
Crystal structure of ASK1 kinase domain with a potent inhibitor (analog 13)
Analyse Crystal structure of ASK1 kinase domain with a potent inhibitor (analog 13) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VIO
- Type
- protein
- Length
- 1,084 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitogen-activated protein kinase kinase kinase 5
- EC
- 2.7.11.25
- UniProt
- Q99683
- Ligands
- 9E4
- Pockets
- 15 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Mitogen-activated protein kinase kinase kinase 5 (EC 2.7.11.25) | protein | 271 | 38% helix, 20% strand | Q99683 |
Ligands and binding sites
- 9E4 · 4-methoxy-N~1~-methyl-N~3~-{6-[4-(propan-2-yl)-4H-1,2, 4-triazol-3-yl]pyridin-2-yl}benzene-1,3-dicarboxamide · ligand · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 196 | 0.64 | 0.84 | 25 | 9E4 |
| 2 | 193 | 0.63 | 0.84 | 27 | 9E4 |
| 3 | 181 | 0.63 | 0.84 | 26 | 9E4 |
| 4 | 188 | 0.62 | 0.83 | 25 | empty |
| 5 | 158 | 0.47 | 0.77 | 24 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1014 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 981 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 105 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5VIO · Crystal structure of ASK1 kinase domain with a potent inhibitor (analog 13) · the same entry in another collection · chain C against C, TM-score 1.00
- Q99683 · AlphaFold monomer V2.0 prediction for mitogen-activated protein kinase kinase kinase 5… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q99683
- Elsewhere: RCSB PDB 5VIO · PDBe 5VIO · UniProt Q99683
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.