Research workbench
Achiral, cheap and potent inhibitors of plasmepsins II
Analyse Achiral, cheap and potent inhibitors of plasmepsins II in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IGY
- Type
- protein
- Length
- 658 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plasmepsin-2
- EC
- 3.4.23.39
- UniProt
- P46925
- Ligands
- A2T
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 12% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Plasmepsin-2 (EC 3.4.23.39) | protein | 329 | 12% helix, 49% strand | P46925 |
Ligands and binding sites
- A2T · N-[1-(3-methylbutyl)piperidin-4-yl]-N-{4-[methyl(pyridin-4-yl)amino]benzyl}-4-pentylbenzamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 603 | 0.68 | 0.77 | 71 | A2T |
| 2 | 455 | 0.65 | 0.77 | 50 | A2T |
| 3 | 428 | 0.63 | 0.77 | 49 | empty |
| 4 | 179 | 0.57 | 0.81 | 31 | empty |
| 5 | 128 | 0.47 | 0.78 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 657 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
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 P46925
- Elsewhere: RCSB PDB 2IGY · PDBe 2IGY · UniProt P46925
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