MolNFT v1 · #171267 · protein
Full length open-form sodium channel navms F208L in complex with cannabidiol (cbd)
6YZ0 · Ion transport protein: “Full length open-form sodium channel navms F208L in complex with cannabidiol (cbd)”. X-ray diffraction, 3 ligands (2CV, CD0, NA), 2 pockets (best druggability 0.49). MolNFT v1 #171267 on GenesisL1: 3D…
- PDB
- 6YZ0
- Type
- protein
- Length
- 257 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ion transport protein
- UniProt
- A0L5S6
- Ligands
- 2CV, CD0, NA
- Pockets
- 2 · best druggability 0.49
Structure
x-ray diffraction · 1 distinct chain · 82% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ion transport protein | protein | 257 | 82% helix, 0% strand | A0L5S6 |
Ligands and binding sites
- 2CV · Hega-10 · ligand · chains A
- CD0 · 2-[(1R,2R,5S)-5-methyl-2-(prop-1-en-2-yl)cyclohexyl]-5-pentylbenzene-1,3-diol · ligand · chains A
- NA · Sodium ion · metal · 3 copies · chains A
- 12P · Dodecaethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 164 | 0.49 | 0.77 | 17 | empty |
| 2 | 55 | 0.36 | 0.79 | 13 | empty |
Compared structures
- 6YZ0 · Full length Open-form Sodium Channel NavMs F208L in complex with Cannabidiol (CBD) · the same entry in another collection · chain A against A, TM-score 1.00
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 A0L5S6
- Elsewhere: RCSB PDB 6YZ0 · PDBe 6YZ0 · UniProt A0L5S6
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