MolNFT v1 · #100695 · protein
Tailoring small molecules for an allosteric site on procaspase-6: CPD1
4N5D: “Tailoring small molecules for an allosteric site on procaspase-6: CPD1”. X-ray diffraction, 2 ligands (2FQ, PO4), 4 pockets (best druggability 0.49). MolNFT v1 #100695 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4N5D
- Type
- protein
- Length
- 500 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
- 2FQ, PO4
- Pockets
- 4 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Caspase-6 (EC 3.4.22.59) | protein | 257 | 27% helix, 25% strand | P55212 |
| B | Caspase-6 (EC 3.4.22.59) | protein | 243 | 28% helix, 28% strand | P55212 |
Ligands and binding sites
- 2FQ · 6-amino-2,8-dimethylpyrido[2,3-d]pyrimidin-7(8H)-one · ligand · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 82 | 0.49 | 0.83 | 23 | empty |
| 2 | 85 | 0.37 | 0.76 | 19 | empty |
| 3 | 64 | 0.32 | 0.76 | 19 | MPD |
| 4 | 57 | 0.31 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1584 Ų buried · 21 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 4N5D · PDBe 4N5D · UniProt P55212
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