Research workbench
Mechanistic and structural understanding of uncompetitive inhibitors of caspase-6
Analyse Mechanistic and structural understanding of uncompetitive inhibitors of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HVA
- Type
- protein
- Length
- 487 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Caspase-6; Veid inhibitor
- EC
- 3.4.22.59
- UniProt
- P55212
- Ligands
- PHQ, 4HV
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Caspase-6 (EC 3.4.22.59) | protein | 238 | 30% helix, 24% strand | P55212 |
| B | Caspase-6 (EC 3.4.22.59) | protein | 241 | 28% helix, 24% strand | P55212 |
| C, D | Veid inhibitor | protein | 4 | 0% helix, 50% strand | — |
Ligands and binding sites
- PHQ · benzyl chlorocarbonate · ligand · 2 copies · chains A, C, B, D
- 4HV · N-[(2R)-1-(3-cyanophenyl)-3-hydroxypropan-2-yl]-5-(3,4-dimethoxyphenyl)furan-3-carboxamide · ligand · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 504 | 0.75 | 0.83 | 54 | empty |
| 2 | 117 | 0.39 | 0.75 | 22 | empty |
| 3 | 99 | 0.38 | 0.76 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2366 Ų buried · 36 hydrogen bonds · protein-protein
- A–C · 474 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 473 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, nonstandard).
Compared structures
- 4HVA · Mechanistic and Structural Understanding of Uncompetitive Inhibitors of Caspase-6 · the same entry in another collection · chain A against A, TM-score 1.00
- P55212 · AlphaFold monomer V2.0 prediction for caspase-6 (P55212) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P55212
- Elsewhere: RCSB PDB 4HVA · PDBe 4HVA · UniProt P55212
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