Research workbench
Small molecule inhibitors of the LEDGF site of HIV type 1 integrase identified by fragment screening and structure based drug design
Analyse Small molecule inhibitors of the LEDGF site of HIV type 1 integrase identified… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZT0
- Type
- protein
- Length
- 298 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.95
- Source
- HUMAN IMMUNODEFICIENCY VIRUS
- Molecule
- Integrase
- EC
- 2.7.7.-
- UniProt
- Q76353
- Ligands
- ZT0, SO4
- Pockets
- 7 · best druggability 0.64
Structure
x-ray diffraction · resolution 1.95 · 1 distinct chain · 53% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Integrase (EC 2.7.7.-) | protein | 149 | 53% helix, 21% strand | Q76353 |
Ligands and binding sites
- ZT0 · (4-carboxy-1,3-benzodioxol-5-yl)-N-{2-[(4-methoxybenzyl)carbamoyl]benzyl}-N-methylmethanaminium · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 241 | 0.64 | 0.82 | 28 | empty |
| 2 | 190 | 0.48 | 0.76 | 36 | empty |
| 3 | 125 | 0.47 | 0.78 | 18 | ZT0 |
| 4 | 118 | 0.47 | 0.79 | 26 | empty |
| 5 | 111 | 0.46 | 0.79 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1477 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 3ZT0 · Small molecule inhibitors of the ledgf site of HIV type 1 integrase identified 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 3ZT0 · PDBe 3ZT0 · UniProt Q76353
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