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
- 3ZSR
- Type
- protein
- Length
- 298 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrase
- EC
- 2.7.7.-
- UniProt
- Q76353
- Ligands
- O3N, SO4, CL
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 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
- O3N · (2S)-2-(2-carboxyethyl)-6-{[{2-[(cyclohexylmethyl)carbamoyl]benzyl}(prop-2-en-1-yl)amino]methyl}-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 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 | 462 | 0.69 | 0.80 | 55 | SO4, O3N |
| 2 | 190 | 0.48 | 0.76 | 32 | empty |
| 3 | 111 | 0.47 | 0.80 | 26 | CL |
| 4 | 102 | 0.45 | 0.79 | 25 | CL |
| 5 | 146 | 0.44 | 0.76 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 1456 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 3ZSR · 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 3ZSR · PDBe 3ZSR · UniProt Q76353
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.