Research workbench
Crystal structure of the complex of caspase-3 with a pryazinone inhibitor
Analyse Crystal structure of the complex of caspase-3 with a pryazinone inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RHJ
- Type
- protein
- Length
- 462 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Caspase-3
- EC
- 3.4.22.-
- UniProt
- P42574
- Ligands
- PZN
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Caspase-3 (EC 3.4.22.-) | protein | 140 | 27% helix, 31% strand | P42574 |
| B, D | Caspase-3 (EC 3.4.22.-) | protein | 91 | 34% helix, 19% strand | P42574 |
Ligands and binding sites
- PZN · 3-(2-{5-tert-butyl-3-[(4-methyl-furazan-3-ylmethyl)-amino]-2-oxo-2H-pyrazin-1-yl}-butyrylamino)-5-(hexyl-methyl-amino)-4-oxo-pentanoic acid anion · ligand · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 392 | 0.70 | 0.82 | 45 | empty |
| 2 | 158 | 0.43 | 0.74 | 25 | PZN |
| 3 | 119 | 0.41 | 0.75 | 19 | PZN |
| 4 | 55 | 0.30 | 0.75 | 17 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2184 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 2173 Ų buried · 32 hydrogen bonds · protein-protein
- B–D · 1373 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 383 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 358 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
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 1RHJ · PDBe 1RHJ · UniProt P42574
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