Research workbench
Crystal structure of procaspase-8 in complex with covalent small molecule inhibitor 63-R
Analyse Crystal structure of procaspase-8 in complex with covalent small molecule… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PX9
- Type
- protein
- Length
- 1,251 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Caspase-8
- EC
- 3.4.22.61
- UniProt
- Q14790
- Ligands
- 63R
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 6 distinct chains · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Caspase-8 (EC 3.4.22.61) | protein | 209 | 32% helix, 21% strand | Q14790 |
| B | Caspase-8 (EC 3.4.22.61) | protein | 207 | 35% helix, 24% strand | Q14790 |
| C | Caspase-8 (EC 3.4.22.61) | protein | 206 | 30% helix, 22% strand | Q14790 |
| D | Caspase-8 (EC 3.4.22.61) | protein | 210 | 30% helix, 21% strand | Q14790 |
| E | Caspase-8 (EC 3.4.22.61) | protein | 210 | 32% helix, 20% strand | Q14790 |
| F | Caspase-8 (EC 3.4.22.61) | protein | 209 | 34% helix, 23% strand | Q14790 |
Ligands and binding sites
- 63R · N-{(3R)-1-[4-(morpholin-4-yl)benzene-1-carbonyl]piperidin-3-yl}-N-phenylacetamide · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 279 | 0.70 | 0.85 | 38 | empty |
| 2 | 128 | 0.65 | 0.88 | 26 | empty |
| 3 | 141 | 0.53 | 0.81 | 23 | empty |
| 4 | 66 | 0.50 | 0.85 | 18 | empty |
| 5 | 106 | 0.48 | 0.80 | 22 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1449 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1442 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 1427 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 202 Ų buried · 2 hydrogen bonds · protein-protein
- A–F · 164 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6PX9 · Crystal structure of procaspase-8 in complex with covalent small molecule inhibitor 63-R · the same entry in another collection · chain F against F, TM-score 1.00
- Q14790 · AlphaFold monomer V2.0 prediction for caspase-8 (Q14790) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 6PX9 · PDBe 6PX9 · UniProt Q14790
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