Research workbench
Structural basis for a new mechanism of inhibition of HIV integrase identified by fragment screening and structure based design
Analyse Structural basis for a new mechanism of inhibition of HIV integrase identified… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NF9
- Type
- protein
- Length
- 298 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrase
- UniProt
- Q76353
- Ligands
- CD9, SO4
- Pockets
- 7 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Integrase | protein | 149 | 53% helix, 21% strand | Q76353 |
Ligands and binding sites
- CD9 · 5-[(6-chloro-2-oxo-2,3-dihydro-1H-indol-1-yl)methyl]-1,3-benzodioxole-4-carboxylic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 11 copies · chains A, B
- ACY · Acetic acid · additive · 6 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
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 | 236 | 0.66 | 0.83 | 30 | SO4 |
| 2 | 87 | 0.48 | 0.82 | 21 | ACY |
| 3 | 224 | 0.47 | 0.74 | 40 | CD9 |
| 4 | 229 | 0.47 | 0.74 | 38 | CD9 |
| 5 | 109 | 0.47 | 0.80 | 23 | ACY |
Interfaces
1 interface between chains.
- A–B · 1506 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 3NF9 · Structural basis for a new mechanism of inhibition of HIV 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 3NF9 · PDBe 3NF9 · UniProt Q76353
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