MolNFT v1 · #87913 · protein
Interrogating HIV integrase for compounds that bind- a sampl challenge
4CF8: “Interrogating HIV integrase for compounds that bind- a sampl challenge”. X-ray diffraction, 3 ligands (V7H, SO4, CL), 6 pockets (best druggability 0.66). MolNFT v1 #87913 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4CF8
- Type
- protein
- Length
- 298 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrase
- EC
- 2.7.7.7
- UniProt
- Q76353
- Ligands
- V7H, SO4, CL
- Pockets
- 6 · 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 (EC 2.7.7.7) | protein | 149 | 53% helix, 21% strand | Q76353 |
Ligands and binding sites
- V7H · (2S)-2-(3-hydroxy-3-oxopropyl)-6-[[[2-[(phenylmethyl)carbamoyl]phenyl]methylamino]methyl]-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
- ACY · Acetic acid · additive · 5 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 372 | 0.66 | 0.80 | 42 | ACY, V7H |
| 2 | 95 | 0.48 | 0.81 | 24 | ACY |
| 3 | 99 | 0.48 | 0.81 | 24 | ACY |
| 4 | 114 | 0.47 | 0.78 | 18 | V7H |
| 5 | 149 | 0.44 | 0.76 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 1438 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 4CF8 · 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 4CF8 · PDBe 4CF8 · UniProt Q76353
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