Research workbench
Crystal structures of caspase-3 with bound isoquinoline-1,3,4-trione derivative inhibitors
Analyse Crystal structures of caspase-3 with bound isoquinoline-1,3,4-trione derivative… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DEK
- Type
- protein
- Length
- 936 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Caspase-3
- EC
- 3.4.22.56
- UniProt
- P42574
- Ligands
- RXD
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Caspase-3 (EC 3.4.22.56) | protein | 233 | 30% helix, 27% strand | P42574 |
| B, C | Caspase-3 (EC 3.4.22.56) | protein | 235 | 28% helix, 24% strand | P42574 |
| D | Caspase-3 (EC 3.4.22.56) | protein | 233 | 29% helix, 23% strand | P42574 |
Ligands and binding sites
- RXD · N-[3-(2-fluoroethoxy)phenyl]-N'-(1,3,4-trioxo-1,2,3,4-tetrahydroisoquinolin-6-yl)butanediamide · ligand · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 839 | 0.69 | 0.75 | 79 | RXD |
| 2 | 261 | 0.63 | 0.81 | 31 | empty |
| 3 | 281 | 0.62 | 0.80 | 32 | empty |
| 4 | 103 | 0.38 | 0.75 | 18 | empty |
| 5 | 89 | 0.37 | 0.75 | 20 | empty |
Interfaces
5 interfaces between chains.
- C–D · 2229 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 2201 Ų buried · 42 hydrogen bonds · protein-protein
- A–C · 773 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 59 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 19 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation).
Compared structures
- 3DEK · Crystal Structures of Caspase-3 with Bound Isoquinoline-1,3,4-trione Derivative Inhibitors · the same entry in another collection · chain D against D, TM-score 1.00
- P42574 · AlphaFold monomer V2.0 prediction for caspase-3 (P42574) · 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 P42574
- Elsewhere: RCSB PDB 3DEK · PDBe 3DEK · UniProt P42574
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