MolNFT v1 · #48613 · protein
HIV-1 pr mutant in complex with nelfinavir
2PYM · Protease retropepsin: “HIV-1 pr mutant in complex with nelfinavir”. X-ray diffraction, 1 ligand (1UN), 1 pocket (best druggability 0.71). MolNFT v1 #48613 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2PYM
- Type
- protein
- Length
- 198 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protease retropepsin
- EC
- 3.4.23.16
- UniProt
- P03367
- Ligands
- 1UN
- Pockets
- 1 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protease retropepsin (EC 3.4.23.16) | protein | 99 | 7% helix, 55% strand | P03367 |
Ligands and binding sites
- 1UN · 2-[2-hydroxy-3-(3-hydroxy-2-methyl-benzoylamino)-4-phenyl sulfanyl-butyl]-decahydro-isoquinoline-3-carboxylic acid tert-butylamide · 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 | 393 | 0.71 | 0.83 | 33 | 1UN |
Interfaces
1 interface between chains.
- A–B · 1835 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 2PYM · HIV-1 PR mutant in complex with nelfinavir · 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 2PYM · PDBe 2PYM · UniProt P03367
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