MolNFT v1 · #137260 · protein
HIV protease (pr) in open form with MG2+ in active site and hive-9 in eye site
5VJ3: “HIV protease (pr) in open form with MG2+ in active site and hive-9 in eye site”. X-ray diffraction, 2 ligands (HV9, MG), 2 pockets (best druggability 0.49). MolNFT v1 #137260 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5VJ3
- Type
- protein
- Length
- 99 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protease
- EC
- 3.4.23.16
- UniProt
- Q8Q8V9
- Ligands
- HV9, MG
- Pockets
- 2 · best druggability 0.49
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protease (EC 3.4.23.16) | protein | 99 | 4% helix, 49% strand | Q8Q8V9 |
Ligands and binding sites
- HV9 · 4-methyl-N-({1-[4-(trifluoromethyl)pyrimidin-2-yl]piperidin-4-yl}carbamoyl)benzene-1-sulfonamide · ligand · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 158 | 0.49 | 0.77 | 20 | empty |
| 2 | 76 | 0.33 | 0.74 | 20 | empty |
Compared structures
- 5VJ3 · HIV Protease (PR) in open form with Mg2+ in active site and HIVE-9 in eye site · 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 Q8Q8V9
- Elsewhere: RCSB PDB 5VJ3 · PDBe 5VJ3 · UniProt Q8Q8V9
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