MolNFT v1 · #87906 · protein
Interrogating HIV integrase for compounds that bind- a sampl challenge
4CF1: “Interrogating HIV integrase for compounds that bind- a sampl challenge”. X-ray diffraction, 2 ligands (IY7, SO4), 5 pockets (best druggability 0.64). MolNFT v1 #87906 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4CF1
- Type
- protein
- Length
- 299 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrase
- EC
- 2.7.7.7
- UniProt
- Q76353
- Ligands
- IY7, SO4
- Pockets
- 5 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrase (EC 2.7.7.7) | protein | 149 | 53% helix, 21% strand | Q76353 |
| B | Integrase (EC 2.7.7.7) | protein | 150 | 53% helix, 21% strand | Q76353 |
Ligands and binding sites
- IY7 · (2s)-6-[[(1r,2s)-2-(5-azanylpentanoylamino)-2,3-dihydro-1h-inden-1-yl]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 · 8 copies · chains A, B
- ACT · Acetate ion · additive · 3 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 420 | 0.64 | 0.77 | 48 | ACT, IY7 |
| 2 | 102 | 0.51 | 0.82 | 20 | ACT |
| 3 | 94 | 0.49 | 0.82 | 20 | empty |
| 4 | 174 | 0.46 | 0.75 | 32 | empty |
| 5 | 119 | 0.41 | 0.76 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1508 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 4CF1 · 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 4CF1 · PDBe 4CF1 · UniProt Q76353
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