Research workbench
Rapid development of potent inhibitors of the HIV integrase-LEDGF interaction by fragment-linking using off-rate screening
Analyse Rapid development of potent inhibitors of the HIV integrase-LEDGF interaction… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LQP
- Type
- protein
- Length
- 289 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.07
- Source
- Human immunodeficiency virus 1
- Molecule
- Integrase
- UniProt
- Q76353
- Ligands
- YAV, SO4, IOD
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · resolution 2.07 · 2 distinct chains · 46% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrase | protein | 145 | 46% helix, 21% strand | Q76353 |
| B | Integrase | protein | 144 | 47% helix, 22% strand | Q76353 |
Ligands and binding sites
- YAV · 2-[2-[2-[3-[2-[2-[2-[[3-[2-[3-(2-hydroxy-2-oxoethyl)-5-methyl-1-benzofuran-2-yl]ethynyl]phenyl]carbonylamino]ethoxy]ethoxy]ethylcar bamoyl]phenyl]ethynyl]-5-methyl-1-benzofuran-3-yl]ethanoic acid · ligand · chains A, B
- SO4 · Sulfate ion · ion · 12 copies · chains A, B
- IOD · Iodide ion · ion · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 277 | 0.64 | 0.81 | 39 | IOD, SO4, YAV |
| 2 | 123 | 0.44 | 0.77 | 24 | empty |
| 3 | 114 | 0.43 | 0.77 | 21 | SO4 |
| 4 | 89 | 0.41 | 0.78 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1571 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 7LQP · Rapid development of potent inhibitors of the HIV integrase-ledgf interaction by… · 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 Q76353
- Elsewhere: RCSB PDB 7LQP · PDBe 7LQP · UniProt Q76353
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