MolNFT v1 · #100911 · protein
Tailoring small molecules for an allosteric site on procaspase-6
4NBK: “Tailoring small molecules for an allosteric site on procaspase-6”. X-ray diffraction, 2 ligands (2J5, PO4), 3 pockets (best druggability 0.50). MolNFT v1 #100911 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4NBK
- Type
- protein
- Length
- 499 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Caspase-6
- EC
- 3.4.22.59
- UniProt
- P55212
- Ligands
- 2J5, PO4
- Pockets
- 3 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Caspase-6 (EC 3.4.22.59) | protein | 256 | 28% helix, 25% strand | P55212 |
| B | Caspase-6 (EC 3.4.22.59) | protein | 243 | 28% helix, 26% strand | P55212 |
Ligands and binding sites
- 2J5 · 2-{[(3-methylpyridin-2-yl)amino]methyl}phenol · ligand · chains A, B
- PO4 · Phosphate ion · ion · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 135 | 0.50 | 0.79 | 25 | 2J5 |
| 2 | 100 | 0.39 | 0.76 | 20 | PO4 |
| 3 | 59 | 0.32 | 0.76 | 19 | PO4 |
Interfaces
1 interface between chains.
- A–B · 1634 Ų buried · 20 hydrogen bonds · protein-protein
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 P55212
- Elsewhere: RCSB PDB 4NBK · PDBe 4NBK · UniProt P55212
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