Research workbench
X-ray structure of D25N chemical analogue of HIV-1 protease complexed with ketomethylene isostere inhibitor
Analyse X-ray structure of D25N chemical analogue of HIV-1 protease complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DCK
- Type
- protein
- Length
- 198 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chemical analogue HIV-1 protease
- EC
- 3.4.23.16
- Ligands
- KVI
- Pockets
- 1 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Chemical analogue HIV-1 protease (EC 3.4.23.16) | protein | 99 | 4% helix, 56% strand | — |
Ligands and binding sites
- KVI · (2S)-2-{[(2R,5S)-5-{[(2S,3S)-2-{[(2S,3R)-2-(acetylamino)-3-hydroxybutanoyl]amino}-3-methylpentanoyl]amino}-2-butyl-4-oxononanoyl]amino}-N~1~-[(2S)-1-amino-5-carbamimidamido-1-oxopentan-2-yl]pentanediamide · ligand · 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 | 385 | 0.71 | 0.83 | 34 | KVI |
Interfaces
1 interface between chains.
- A–B · 1812 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (nonstandard, alkylation).
Compared structures
- 3DCK · X-ray structure of D25N chemical analogue of HIV-1 protease complexed with ketomethylene… · 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
- Elsewhere: RCSB PDB 3DCK · PDBe 3DCK
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.