MolNFT v1 · #55354 · protein
Trypanosoma brucei PTR1 in complex with inhibitor WHF30
2YHU · Pteridine reductase: “Trypanosoma brucei PTR1 in complex with inhibitor WHF30”. X-ray diffraction, 2 ligands (NDP, WHF), 9 pockets (best druggability 0.84). MolNFT v1 #55354 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2YHU
- Type
- protein
- Length
- 1,002 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pteridine reductase
- EC
- 1.5.1.33
- UniProt
- O76290
- Ligands
- NDP, WHF
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pteridine reductase (EC 1.5.1.33) | protein | 251 | 46% helix, 15% strand | O76290 |
| B | Pteridine reductase (EC 1.5.1.33) | protein | 250 | 47% helix, 15% strand | O76290 |
| C | Pteridine reductase (EC 1.5.1.33) | protein | 252 | 48% helix, 14% strand | O76290 |
| D | Pteridine reductase (EC 1.5.1.33) | protein | 249 | 47% helix, 15% strand | O76290 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- WHF · 3-(5-amino-1,3,4-thiadiazol-2-yl)-1-thiophen-2-ylpropan-1-one · ligand · 4 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1159 | 0.84 | 0.85 | 69 | empty |
| 2 | 629 | 0.77 | 0.83 | 47 | NDP, WHF |
| 3 | 619 | 0.77 | 0.83 | 49 | NDP, WHF |
| 4 | 604 | 0.77 | 0.83 | 48 | NDP, WHF |
| 5 | 574 | 0.75 | 0.82 | 46 | NDP, WHF |
Interfaces
6 interfaces between chains.
- A–C · 1911 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 1885 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1430 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1418 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 567 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation).
Compared structures
- 2YHU · Trypanosoma brucei PTR1 in complex with inhibitor WHF30 · 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 O76290
- Elsewhere: RCSB PDB 2YHU · PDBe 2YHU · UniProt O76290
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