Research workbench
Novel inhibitors of plasmodium falciparum dutpase provide a platform for anti-malarial drug design
Analyse Novel inhibitors of plasmodium falciparum dutpase provide a platform for… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VYQ
- Type
- protein
- Length
- 418 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxyuridine 5'-triphosphate nucleotidohydrolase
- EC
- 3.6.1.23
- UniProt
- Q8II92
- Ligands
- DUX
- Pockets
- 6 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 139 | 9% helix, 43% strand | Q8II92 |
| B | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 140 | 9% helix, 43% strand | Q8II92 |
| C | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 139 | 9% helix, 42% strand | Q8II92 |
Ligands and binding sites
- DUX · 2,3-deoxy-3-fluoro-5-O-trityluridine · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 320 | 0.66 | 0.82 | 38 | empty |
| 2 | 543 | 0.65 | 0.77 | 62 | empty |
| 3 | 114 | 0.48 | 0.79 | 18 | DUX |
| 4 | 138 | 0.48 | 0.78 | 25 | DUX |
| 5 | 112 | 0.45 | 0.78 | 15 | DUX |
Interfaces
3 interfaces between chains.
- A–C · 1007 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 934 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 655 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1VYQ · Novel inhibitors of Plasmodium Falciparum dUTPase provide a platform for anti-malarial… · 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 Q8II92
- Elsewhere: RCSB PDB 1VYQ · PDBe 1VYQ · UniProt Q8II92
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