Research workbench
Fragment-based approach to the design of ligands targeting a novel site in HIV-1 integrase
Analyse Fragment-based approach to the design of ligands targeting a novel site in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3AO1
- Type
- protein
- Length
- 283 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pol polyprotein
- UniProt
- Q72498
- Ligands
- BZX, CD, SO4
- Pockets
- 5 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pol polyprotein | protein | 141 | 47% helix, 23% strand | Q72498 |
| B | Pol polyprotein | protein | 142 | 51% helix, 23% strand | Q72498 |
Ligands and binding sites
- BZX · 1,3-benzodioxol-5-ol · ligand · 3 copies · chains A, B
- CD · Cadmium ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 153 | 0.48 | 0.77 | 19 | empty |
| 2 | 97 | 0.48 | 0.81 | 24 | BZX |
| 3 | 99 | 0.47 | 0.80 | 22 | BZX |
| 4 | 99 | 0.41 | 0.76 | 16 | empty |
| 5 | 96 | 0.40 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1469 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 3AO1 · Fragment-based approach to the design of ligands targeting a novel site in 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 3AO1 · PDBe 3AO1 · UniProt Q72498
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