Research workbench
5'-diphenyl nucleoside inhibitors of plasmodium falciparum dutpase
Analyse 5'-diphenyl nucleoside inhibitors of plasmodium falciparum dutpase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3T64
- Type
- protein
- Length
- 442 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxyuridine 5'-triphosphate nucleotidohydrolase, putative…
- EC
- 3.6.1.23
- UniProt
- Q8II92
- Ligands
- DU3, SO4
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxyuridine 5'-triphosphate nucleotidohydrolase, putative (EC 3.6.1.23) | protein | 153 | 8% helix, 41% strand | Q8II92 |
| B | Deoxyuridine 5'-triphosphate nucleotidohydrolase, putative (EC 3.6.1.23) | protein | 135 | 10% helix, 46% strand | Q8II92 |
| C | Deoxyuridine 5'-triphosphate nucleotidohydrolase, putative (EC 3.6.1.23) | protein | 151 | 9% helix, 41% strand | Q8II92 |
| F | 5'-(benzhydrylamino)-2',5'-dideoxyuridine | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- DU3 · 2',5'-dideoxy-5'-[(diphenylmethyl)amino]uridine · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 4 copies · chains A, C, 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 | 378 | 0.70 | 0.82 | 37 | empty |
| 2 | 597 | 0.69 | 0.78 | 59 | empty |
| 3 | 209 | 0.55 | 0.78 | 26 | SO4, DU3 |
| 4 | 177 | 0.50 | 0.77 | 23 | DU3, SO4 |
| 5 | 175 | 0.50 | 0.77 | 29 | DU3, SO4 |
Interfaces
5 interfaces between chains.
- A–C · 1014 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 964 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 957 Ų buried · 10 hydrogen bonds · protein-protein
- A–F · 168 Ų buried · 3 hydrogen bonds · protein-protein
- B–F · 158 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3T64 · 5'-Diphenyl Nucleoside Inhibitors of Plasmodium falciparum dUTPase · 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 3T64 · PDBe 3T64 · UniProt Q8II92
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