Research workbench
ASK1 kinase domain in complex with gs-4997
Analyse ASK1 kinase domain in complex with gs-4997 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OYT
- Type
- protein
- Length
- 949 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
- NJV
- Pockets
- 10 · best druggability 0.64
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitogen-activated protein kinase kinase kinase 5 (EC 2.7.11.25) | protein | 222 | 36% helix, 24% strand | Q99683 |
| B | Mitogen-activated protein kinase kinase kinase 5 (EC 2.7.11.25) | protein | 238 | 34% helix, 22% strand | Q99683 |
| C | Mitogen-activated protein kinase kinase kinase 5 (EC 2.7.11.25) | protein | 236 | 35% helix, 23% strand | Q99683 |
| D | Mitogen-activated protein kinase kinase kinase 5 (EC 2.7.11.25) | protein | 253 | 34% helix, 21% strand | Q99683 |
Ligands and binding sites
- NJV · 5-(4-cyclopropyl-1H-imidazol-1-yl)-2-fluoro-4-methyl-N-{6-[4-(propan-2-yl)-4H-1,2,4-triazol-3-yl]pyridin-2-yl}benzamide · ligand · 4 copies · chains A, C, B, D
- ACT · Acetate ion · additive · 9 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 165 | 0.64 | 0.85 | 25 | NJV |
| 2 | 244 | 0.64 | 0.82 | 43 | NJV |
| 3 | 257 | 0.62 | 0.81 | 35 | NJV |
| 4 | 153 | 0.62 | 0.84 | 24 | NJV |
| 5 | 450 | 0.60 | 0.75 | 56 | ACT |
Interfaces
5 interfaces between chains.
- B–D · 1022 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 976 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 317 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 109 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 62 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
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 6OYT · PDBe 6OYT · UniProt Q99683
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