MolNFT v1 · #19234 · protein
Crystal structure of the complex of caspase-8 with the tripeptide ketone inhibitor zevd-dcbmk
1QDU · Caspase-8 alpha-chain: “Crystal structure of the complex of caspase-8 with the tripeptide ketone inhibitor zevd-dcbmk”. X-ray diffraction, 2 ligands (PHQ, 0QE), 11 pockets (best druggability 0.76). MolNFT v1 #19234 on GenesisL1: 3D…
- PDB
- 1QDU
- Type
- protein
- Length
- 1,464 residues
- Chains
- 18
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Caspase-8 alpha-chain; Caspase-8 beta-chain; Phq-glu-val-asp-dichloromethylketone…
- EC
- 3.4.22.-
- UniProt
- Q14790
- Ligands
- PHQ, 0QE
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K | Caspase-8 alpha-chain (EC 3.4.22.-) | protein | 153 | 29% helix, 26% strand | Q14790 |
| B, D, F, H, J, L | Caspase-8 beta-chain (EC 3.4.22.-) | protein | 88 | 30% helix, 24% strand | Q14790 |
| T, U, V, W, X, Y | Phq-glu-val-asp-dichloromethylketone inhibitor | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- PHQ · benzyl chlorocarbonate · ligand · 6 copies · chains B, T, D, U, F, V, H, W, J, X, L, Y
- 0QE · Chloromethane · ion · 6 copies · chains A, T, C, U, E, V, G, W, I, X, K, Y
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 703 | 0.76 | 0.81 | 52 | empty |
| 2 | 701 | 0.74 | 0.80 | 50 | empty |
| 3 | 715 | 0.74 | 0.79 | 54 | empty |
| 4 | 171 | 0.45 | 0.75 | 20 | empty |
| 5 | 131 | 0.43 | 0.76 | 18 | 0QE |
Interfaces
31 interfaces between chains.
- C–D · 2241 Ų buried · 36 hydrogen bonds · protein-protein
- K–L · 2229 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 2225 Ų buried · 37 hydrogen bonds · protein-protein
- E–F · 2219 Ų buried · 34 hydrogen bonds · protein-protein
- G–H · 2214 Ų buried · 38 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 1QDU · Crystal structure of the complex of caspase-8 with the tripeptide ketone inhibitor… · the same entry in another collection · chain H against H, 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 Q14790
- Elsewhere: RCSB PDB 1QDU · PDBe 1QDU · UniProt Q14790
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.