Research workbench
Discovery of novel uracil derivatives as potent human dutpase inhibitors
Analyse Discovery of novel uracil derivatives as potent human dutpase inhibitors in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ARA
- Type
- protein
- Length
- 375 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
- P33316
- Ligands
- MKH, MG
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 125 | 6% helix, 49% strand | P33316 |
Ligands and binding sites
- MKH · 1-[3-({(2R)-2-[hydroxy(diphenyl)methyl]pyrrolidin-1-yl}sulfonyl)propyl]pyrimidine-2,4(1H,3H)-dione · ligand · 3 copies · chains A, C, B
- MG · Magnesium ion · metal · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 114 | 0.79 | 0.99 | 26 | empty |
| 2 | 164 | 0.48 | 0.77 | 31 | MKH |
| 3 | 173 | 0.47 | 0.76 | 32 | MKH |
| 4 | 157 | 0.47 | 0.76 | 30 | MKH |
Interfaces
3 interfaces between chains.
- A–B · 1734 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 1732 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 1674 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 3ARA · Discovery of Novel Uracil Derivatives as Potent Human dUTPase Inhibitors · the same entry in another collection · chain A against A, TM-score 1.00
- P33316 · AlphaFold monomer V2.0 prediction for deoxyuridine 5'-triphosphate nucleotidohydrolase… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P33316
- Elsewhere: RCSB PDB 3ARA · PDBe 3ARA · UniProt P33316
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