MolNFT v1 · #82537 · protein
HIV-1 in core domain in complex with (3R)-3,4-dihydro-2H-chromen-3- ylmethanol
3VQ8 · Pol polyprotein: “HIV-1 in core domain in complex with (3R)-3,4-dihydro-2H-chromen-3- ylmethanol”. X-ray diffraction, 4 ligands (BCU, CD, SO4), 5 pockets (best druggability 0.54). MolNFT v1 #82537 on GenesisL1: 3D structure, binding…
- PDB
- 3VQ8
- Type
- protein
- Length
- 269 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pol polyprotein
- UniProt
- Q72498
- Ligands
- BCU, CD, SO4, CL
- Pockets
- 5 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pol polyprotein | protein | 136 | 51% helix, 21% strand | Q72498 |
| B | Pol polyprotein | protein | 133 | 50% helix, 20% strand | Q72498 |
Ligands and binding sites
- BCU · (3R)-3,4-dihydro-2H-chromen-3-ylmethanol · ligand · 2 copies · chains A, B
- CD · Cadmium ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 187 | 0.54 | 0.79 | 19 | empty |
| 2 | 94 | 0.50 | 0.82 | 24 | empty |
| 3 | 99 | 0.49 | 0.81 | 24 | empty |
| 4 | 103 | 0.47 | 0.79 | 14 | BCU |
| 5 | 98 | 0.46 | 0.79 | 15 | BCU |
Interfaces
1 interface between chains.
- A–B · 1474 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 3VQ8 · HIV-1 IN core domain in complex with (3R)-3,4-dihydro-2H-chromen-3-ylmethanol · 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 Q72498
- Elsewhere: RCSB PDB 3VQ8 · PDBe 3VQ8 · UniProt Q72498
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.