Research workbench
Crystal structure of the complex of caspase-3 with a cinnamic acid methyl ester inhibitor
Analyse Crystal structure of the complex of caspase-3 with a cinnamic acid methyl ester… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RHR
- Type
- protein
- Length
- 231 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Caspase-3
- EC
- 3.4.22.-
- UniProt
- P42574
- Ligands
- CNE
- Pockets
- 1 · best druggability 0.42
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Caspase-3 (EC 3.4.22.-) | protein | 140 | 23% helix, 24% strand | P42574 |
| B | Caspase-3 (EC 3.4.22.-) | protein | 91 | 25% helix, 16% strand | P42574 |
Ligands and binding sites
- CNE · (3S)-5-[(2-chloro-6-fluorobenzyl)sulfanyl]-3-{[N-({2-ethoxy-5-[(1E)-3-methoxy-3-oxoprop-1-enyl]phenyl}acetyl)-D-valyl]amino}-4-oxopentanoic acid · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 117 | 0.42 | 0.76 | 19 | CNE |
Interfaces
1 interface between chains.
- A–B · 2116 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 1RHR · Crystal structure of the complex of caspase-3 with a cinnamic acid methyl ester inhibitor · the same entry in another collection · chain A against A, 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 1RHR · PDBe 1RHR · UniProt P42574
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