MolNFT v1 · #72662 · protein
Structural basis for a new mechanism of inhibition of HIV integrase identified by fragment screening and structure based design
3NF8: “Structural basis for a new mechanism of inhibition of HIV integrase identified by fragment screening and…”. X-ray diffraction, 2 ligands (CDQ, SO4), 7 pockets (best druggability 0.66). MolNFT v1 #72662 on GenesisL1: 3D structure…
- PDB
- 3NF8
- Type
- protein
- Length
- 298 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrase
- UniProt
- Q76353
- Ligands
- CDQ, SO4
- Pockets
- 7 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Integrase | protein | 149 | 52% helix, 21% strand | Q76353 |
Ligands and binding sites
- CDQ · 6-[(5-chloro-2-oxo-2,3-dihydro-1H-indol-1-yl)methyl]-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid · ligand · 6 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- ACY · Acetic acid · additive · 2 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 226 | 0.66 | 0.84 | 27 | ACY |
| 2 | 175 | 0.53 | 0.79 | 26 | CDQ |
| 3 | 122 | 0.50 | 0.80 | 20 | CDQ |
| 4 | 155 | 0.46 | 0.76 | 27 | CDQ |
| 5 | 102 | 0.43 | 0.77 | 16 | CDQ |
Interfaces
1 interface between chains.
- A–B · 1462 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 3NF8 · 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 3NF8 · PDBe 3NF8 · UniProt Q76353
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