Research workbench
HIV-1 protease in complex with a difluoroketone containing inhibitor A79285
Analyse HIV-1 protease in complex with a difluoroketone containing inhibitor A79285 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DIF
- Type
- protein
- Length
- 198 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 protease
- UniProt
- P03367
- Ligands
- A85
- Pockets
- 1 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | HIV-1 protease | protein | 99 | 4% helix, 54% strand | P03367 |
Ligands and binding sites
- A85 · N-{1-benzyl-2,2-difluoro-3,3-dihydroxy-4-[3-methyl-2-(3-methyl-3-pyridin-2-ylmethyl-ureido)-butyrylamino]-5-phenyl-pentyl}-3-methyl-2-(3-methyl-3-pyridin-2-ylmethyl-ureido)-butyramide · ligand · chains A, B
- BME · Beta-mercaptoethanol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 447 | 0.71 | 0.81 | 39 | A85 |
Interfaces
1 interface between chains.
- A–B · 1820 Ų buried · 36 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (additive adduct).
Compared structures
- 1DIF · HIV-1 protease in complex with a difluoroketone containing inhibitor A79285 · 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 P03367
- Elsewhere: RCSB PDB 1DIF · PDBe 1DIF · UniProt P03367
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