MolNFT v1 · #82543 · protein
HIV-1 in core domain in complex with [1-(4-fluorophenyl)-5-methyl-1H- pyrazol-4-YL]METHANOL
3VQE · Pol polyprotein: “HIV-1 in core domain in complex with [1-(4-fluorophenyl)-5-methyl-1H- pyrazol-4-YL]METHANOL”. X-ray diffraction, 4 ligands (FMQ, CD, SO4), 5 pockets (best druggability 0.50). MolNFT v1 #82543 on GenesisL1: 3D…
- PDB
- 3VQE
- 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
- FMQ, CD, SO4, CL
- Pockets
- 5 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pol polyprotein | protein | 136 | 51% helix, 21% strand | Q72498 |
| B | Pol polyprotein | protein | 133 | 49% helix, 22% strand | Q72498 |
Ligands and binding sites
- FMQ · [1-(4-fluorophenyl)-5-methyl-1H-pyrazol-4-yl]methanol · 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 | 176 | 0.50 | 0.77 | 19 | empty |
| 2 | 98 | 0.49 | 0.82 | 22 | FMQ |
| 3 | 89 | 0.48 | 0.82 | 21 | FMQ |
| 4 | 113 | 0.44 | 0.77 | 16 | empty |
| 5 | 92 | 0.42 | 0.78 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1595 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 3VQE · HIV-1 IN core domain in complex with [1-(4-fluorophenyl)-5-methyl-1H-pyrazol-4-yl]methanol · 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 3VQE · PDBe 3VQE · UniProt Q72498
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