MolNFT v2 · #25822 · protein
Novel plasmepsin II-inhibitor complex
1W6H · Plasmepsin 2: “Novel plasmepsin II-inhibitor complex”. X-ray diffraction at 2.24, 1 ligand (TIT), 4 pockets (best druggability 0.67). MolNFT v2 #25822 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1W6H
- Type
- protein
- Length
- 650 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.24
- Source
- PLASMODIUM FALCIPARUM
- Molecule
- Plasmepsin 2
- EC
- 3.4.23.39
- UniProt
- P46925
- Ligands
- TIT
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · resolution 2.24 · 1 distinct chain · 14% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Plasmepsin 2 (EC 3.4.23.39) | protein | 325 | 14% helix, 47% strand | P46925 |
Ligands and binding sites
- TIT · N-((3S,4S)-5-[(4-bromobenzyl)oxy]-3-hydroxy-4-{[N-(pyridin-2-ylcarbonyl)-L-valyl]amino}pentanoyl)-L-alanyl-L-leucinamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 430 | 0.67 | 0.79 | 48 | TIT |
| 2 | 439 | 0.65 | 0.78 | 47 | TIT |
| 3 | 124 | 0.44 | 0.77 | 21 | empty |
| 4 | 109 | 0.43 | 0.77 | 16 | empty |
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 1W6H · PDBe 1W6H · UniProt P46925
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