MolNFT v1 · #88078 · protein
Interrogating HIV integrase for compounds that bind- a sampl challenge
4CK1: “Interrogating HIV integrase for compounds that bind- a sampl challenge”. X-ray diffraction, 3 ligands (OM1, SO4, CL), 7 pockets (best druggability 0.63). MolNFT v1 #88078 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4CK1
- 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
- OM1, SO4, CL
- Pockets
- 7 · best druggability 0.63
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
- OM1 · (4-carboxy-1,3-benzodioxol-5-yl)methyl-[[2-[(4-methoxyphenyl)methylcarbamoyl]phenyl]methyl]azanium · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 8 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
- ACT · Acetate ion · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 229 | 0.63 | 0.82 | 26 | SO4, ACT |
| 2 | 102 | 0.50 | 0.81 | 24 | SO4 |
| 3 | 108 | 0.49 | 0.81 | 25 | empty |
| 4 | 126 | 0.44 | 0.76 | 17 | OM1 |
| 5 | 115 | 0.43 | 0.76 | 18 | OM1 |
Interfaces
1 interface between chains.
- A–B · 1423 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 4CK1 · 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 4CK1 · PDBe 4CK1 · UniProt Q76353
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