MolNFT v1 · #61140 · protein
X-ray structure of HIV-1 protease and hydrated form of ketomethylene isostere inhibitor
3DCR · Chemical analogue HIV-1 protease: “X-ray structure of HIV-1 protease and hydrated form of ketomethylene isostere inhibitor”. X-ray diffraction, 1 ligand (KVS), 1 pocket (best druggability 0.70). MolNFT v1 #61140 on GenesisL1: 3D…
- PDB
- 3DCR
- 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
- KVS
- Pockets
- 1 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Chemical analogue HIV-1 protease (EC 3.4.23.16) | protein | 99 | 7% helix, 54% strand | — |
Ligands and binding sites
- KVS · N~2~-[(2R,5S)-5-({(2S,3S)-2-[(N-acetyl-L-threonyl) amino]-3-methylpent-4-enoyl}amino)-2-butyl-4,4-dihydroxynonanoyl]-L-glutaminyl-L-argininamide · 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 | 377 | 0.70 | 0.82 | 34 | KVS |
Interfaces
1 interface between chains.
- A–B · 1802 Ų buried · 34 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (nonstandard, alkylation).
Compared structures
- 3DCR · X-ray structure of HIV-1 protease and hydrated form of ketomethylene isostere inhibitor · 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 3DCR · PDBe 3DCR
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.