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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
- 3DEH
- Type
- protein
- Length
- 930 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
- RXA
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Caspase-3 (EC 3.4.22.56) | protein | 233 | 29% helix, 25% strand | P42574 |
| B | Caspase-3 (EC 3.4.22.56) | protein | 235 | 30% helix, 24% strand | P42574 |
| D | Caspase-3 (EC 3.4.22.56) | protein | 229 | 30% helix, 23% strand | P42574 |
Ligands and binding sites
- RXA · isoquinoline-1,3,4(2H)-trione · 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 | 884 | 0.70 | 0.76 | 80 | RXA |
| 2 | 281 | 0.64 | 0.81 | 30 | empty |
| 3 | 293 | 0.64 | 0.80 | 34 | empty |
| 4 | 75 | 0.36 | 0.76 | 20 | empty |
| 5 | 72 | 0.35 | 0.76 | 20 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2202 Ų buried · 42 hydrogen bonds · protein-protein
- C–D · 2071 Ų buried · 39 hydrogen bonds · protein-protein
- A–C · 806 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 53 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 28 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation).
Compared structures
- 3DEH · 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 3DEH · PDBe 3DEH · UniProt P42574
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