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
- 3AO4
- Type
- protein
- Length
- 272 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pol polyprotein
- UniProt
- Q72498
- Ligands
- 833, CD, SO4, CL
- Pockets
- 5 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pol polyprotein | protein | 139 | 50% helix, 21% strand | Q72498 |
| B | Pol polyprotein | protein | 133 | 50% helix, 22% strand | Q72498 |
Ligands and binding sites
- 833 · 3-(1,3-benzodioxol-5-yl)-1-methyl-1H-pyrazol-5-amine · ligand · 2 copies · chains A, B
- CD · Cadmium ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 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 | 157 | 0.50 | 0.78 | 19 | empty |
| 2 | 115 | 0.50 | 0.80 | 22 | 833 |
| 3 | 111 | 0.49 | 0.80 | 23 | 833 |
| 4 | 93 | 0.47 | 0.80 | 15 | empty |
| 5 | 90 | 0.43 | 0.79 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1437 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 3AO4 · 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 3AO4 · PDBe 3AO4 · UniProt Q72498
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