MolNFT v1 · #88080 · protein
Interrogating HIV integrase for compounds that bind- a sampl challenge
4CK3: “Interrogating HIV integrase for compounds that bind- a sampl challenge”. X-ray diffraction, 2 ligands (K1T, SO4), 7 pockets (best druggability 0.64). MolNFT v1 #88080 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4CK3
- 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
- K1T, SO4
- Pockets
- 7 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Integrase (EC 2.7.7.7) | protein | 149 | 54% helix, 20% strand | Q76353 |
Ligands and binding sites
- K1T · 5-[(2S)-2-{[(4-aminobutanoyl)amino]methyl}-4-methylpentyl]-1,3-benzodioxole-4-carboxylic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 7 copies · chains A, B
- ACT · Acetate ion · additive · 4 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 245 | 0.64 | 0.82 | 29 | ACT |
| 2 | 125 | 0.51 | 0.81 | 27 | empty |
| 3 | 126 | 0.50 | 0.80 | 26 | SO4 |
| 4 | 102 | 0.45 | 0.79 | 18 | K1T |
| 5 | 151 | 0.44 | 0.75 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1462 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 4CK3 · 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 4CK3 · PDBe 4CK3 · UniProt Q76353
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