Research workbench
Fragment-based approach to the design of ligands targeting a novel site on HIV-1 integrase
Analyse Fragment-based approach to the design of ligands targeting a novel site on… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3AO5
- Type
- protein
- Length
- 275 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pol polyprotein
- UniProt
- Q72498
- Ligands
- BBY, GLC, FRU, CD, SO4, CL
- Pockets
- 5 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pol polyprotein | protein | 135 | 49% helix, 20% strand | Q72498 |
| B | Pol polyprotein | protein | 140 | 47% helix, 20% strand | Q72498 |
Ligands and binding sites
- BBY · 5-(7-bromo-1,3-benzodioxol-5-yl)-1-methyl-1H-pyrazol-3-amine · ligand · 2 copies · chains A, B
- GLC · alpha-D-glucopyranose · sugar · chains A, B
- FRU · beta-D-fructofuranose · sugar · chains A, B
- CD · Cadmium ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 209 | 0.54 | 0.78 | 24 | GLC, FRU |
| 2 | 120 | 0.52 | 0.81 | 24 | BBY |
| 3 | 111 | 0.50 | 0.81 | 24 | BBY |
| 4 | 99 | 0.46 | 0.79 | 15 | SO4 |
| 5 | 130 | 0.45 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1480 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 3AO5 · Fragment-based approach to the design of ligands targeting a novel site on HIV-1 integrase · 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 3AO5 · PDBe 3AO5 · UniProt Q72498
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