MolNFT v1 · #136730 · protein
Structure-based drug design of novel ASK1 inhibitors using a fully integrated lead optimization strategy
5V24 · Mitogen-activated protein kinase kinase kinase 5: “Structure-based drug design of novel ASK1 inhibitors using a fully integrated lead optimization strategy”. X-ray diffraction, 1 ligand (8V7), 7 pockets (best druggability 0.63).…
- PDB
- 5V24
- Type
- protein
- Length
- 512 residues
- Chains
- 2
- 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
- 8V7
- Pockets
- 7 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitogen-activated protein kinase kinase kinase 5 (EC 2.7.11.25) | protein | 249 | 36% helix, 21% strand | Q99683 |
| B | Mitogen-activated protein kinase kinase kinase 5 (EC 2.7.11.25) | protein | 263 | 40% helix, 21% strand | Q99683 |
Ligands and binding sites
- 8V7 · 2-[4-(propan-2-yl)-4H-1,2,4-triazol-3-yl]-N-(pyridin-2-yl)-1,3-thiazole-4-carboxamide · 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 | 121 | 0.63 | 0.87 | 20 | empty |
| 2 | 171 | 0.62 | 0.84 | 22 | 8V7 |
| 3 | 195 | 0.61 | 0.83 | 27 | 8V7 |
| 4 | 194 | 0.51 | 0.77 | 28 | empty |
| 5 | 97 | 0.44 | 0.78 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 573 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5V24 · Structure-based drug design of novel ASK1 inhibitors using a fully integrated lead… · the same entry in another collection · chain A against A, 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 B 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 5V24 · PDBe 5V24 · UniProt Q99683
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