MolNFT v1 · #90097 · protein
Crystal structure of the N-terminal domain of HIV-1 capsid in complex with inhibitor BD3
4E91 · Gag protein: “Crystal structure of the N-terminal domain of HIV-1 capsid in complex with inhibitor BD3”. X-ray diffraction, 3 ligands (0OE, 0OF, IOD), 4 pockets (best druggability 0.71). MolNFT v1 #90097 on GenesisL1: 3D structure…
- PDB
- 4E91
- Type
- protein
- Length
- 267 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gag protein
- UniProt
- Q79791
- Ligands
- 0OE, 0OF, IOD
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 62% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gag protein | protein | 131 | 64% helix, 2% strand | Q79791 |
| B | Gag protein | protein | 136 | 60% 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
- 0OF · (3S)-1-ethyl-3-[3-hydroxy-5-(pyridin-3-yl)phenyl]-5-phenyl-7-(trifluoromethyl)-1H-1,5-benzodiazepine-2,4(3H,5H)-dione · ligand · chains A
- IOD · Iodide ion · ion · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 257 | 0.71 | 0.86 | 33 | 0OF |
| 2 | 627 | 0.71 | 0.79 | 75 | 0OE |
| 3 | 206 | 0.68 | 0.85 | 23 | empty |
| 4 | 83 | 0.67 | 0.92 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 769 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4E91 · Crystal Structure of the N-Terminal Domain of HIV-1 Capsid in Complex With Inhibitor BD3 · 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 4E91 · PDBe 4E91 · UniProt Q79791
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