MolNFT v1 · #87918 · protein
Interrogating HIV integrase for compounds that bind- a sampl challenge
4CFD: “Interrogating HIV integrase for compounds that bind- a sampl challenge”. X-ray diffraction, 3 ligands (S8Y, SO4, CL), 7 pockets (best druggability 0.64). MolNFT v1 #87918 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4CFD
- 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
- S8Y, SO4, CL
- Pockets
- 7 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Integrase (EC 2.7.7.7) | protein | 149 | 52% helix, 23% strand | Q76353 |
Ligands and binding sites
- S8Y · 5-[[[(1R)-2-(tert-butylamino)-2-oxidanylidene-1-phenyl-ethyl]carbamoyl-methyl-amino]methyl]-1,3-benzodioxole-4-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 · 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 | 244 | 0.64 | 0.82 | 28 | ACT |
| 2 | 103 | 0.50 | 0.81 | 24 | CL |
| 3 | 93 | 0.47 | 0.81 | 18 | CL |
| 4 | 168 | 0.47 | 0.76 | 33 | empty |
| 5 | 153 | 0.45 | 0.76 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 1495 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 4CFD · 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 4CFD · PDBe 4CFD · UniProt Q76353
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