MolNFT v1 · #90098 · protein
Crystal structure of the N-terminal domain of HIV-1 capsid in complex with inhibitor BM4
4E92 · Gag protein: “Crystal structure of the N-terminal domain of HIV-1 capsid in complex with inhibitor BM4”. X-ray diffraction, 2 ligands (0OE, 0OG), 5 pockets (best druggability 0.73). MolNFT v1 #90098 on GenesisL1: 3D structure…
- PDB
- 4E92
- Type
- protein
- Length
- 280 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gag protein
- UniProt
- Q79791
- Ligands
- 0OE, 0OG
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 59% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Gag protein | protein | 140 | 59% helix, 4% strand | Q79791 |
Ligands and binding sites
- 0OE · 4-{2-[5-(3-chlorophenyl)-1H-pyrazol-4-yl]-1-[3-(1H-imidazol-1-yl)propyl]-1H-benzimidazol-5-yl}benzoic acid · ligand · 2 copies · chains A, B
- 0OG · 3-{5-[3-ethyl-5-(5-methylfuran-2-yl)-1H-pyrazol-1-yl]-1-[(6-oxo-1,6-dihydropyridin-3-yl)methyl]-1H-benzimidazol-2-yl}-4-hydroxybenzoic acid · ligand · 2 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 771 | 0.73 | 0.78 | 78 | 0OE |
| 2 | 123 | 0.69 | 0.90 | 18 | 0OG |
| 3 | 140 | 0.68 | 0.88 | 22 | 0OG |
| 4 | 178 | 0.68 | 0.87 | 26 | empty |
| 5 | 54 | 0.27 | 0.73 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 784 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4E92 · Crystal Structure of the N-Terminal Domain of HIV-1 Capsid in Complex With Inhibitor BM4 · 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 Q79791
- Elsewhere: RCSB PDB 4E92 · PDBe 4E92 · UniProt Q79791
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