Research workbench
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Analyse Interrogating HIV integrase for compounds that bind- a SAMPL challenge in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CEQ
- Type
- protein
- Length
- 298 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.7
- Source
- HUMAN IMMUNODEFICIENCY VIRUS 1
- Molecule
- Integrase
- EC
- 2.7.7.7
- UniProt
- Q76353
- Ligands
- QCH, SO4, CL
- Pockets
- 7 · best druggability 0.66
Structure
x-ray diffraction · resolution 1.7 · 1 distinct chain · 54% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Integrase (EC 2.7.7.7) | protein | 149 | 54% helix, 21% strand | Q76353 |
Ligands and binding sites
- QCH · (2S)-6-[[[2-(cyclohexylmethylcarbamoyl)phenyl]methyl-methyl-amino]methyl]-2-(3-hydroxy-3-oxopropyl)-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
- ACT · Acetate ion · additive · chains A, B
- DMS · Dimethyl sulfoxide · additive · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 229 | 0.66 | 0.84 | 28 | ACT, DMS |
| 2 | 106 | 0.50 | 0.81 | 25 | CL |
| 3 | 100 | 0.45 | 0.79 | 20 | CL |
| 4 | 170 | 0.45 | 0.75 | 32 | empty |
| 5 | 153 | 0.43 | 0.75 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 1474 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 4CEQ · Interrogating HIV integrase for compounds that bind- a sampl challenge · 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 4CEQ · PDBe 4CEQ · UniProt Q76353
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