Research workbench
Crystal structure of trypanothione reductase from trypanosoma brucei in complex with inhibitor RD117 1-[2-(piperazin-1-YL)ETHYL]-5-{5-[1- (pyrrolidin-1-YL)CYCLOHEXYL]-1,3-thiazol-2-yl}-1H-indole
Analyse Crystal structure of trypanothione reductase from trypanosoma brucei in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BTL
- Type
- protein
- Length
- 984 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trypanothione reductase
- EC
- 1.8.1.12
- UniProt
- Q389T8
- Ligands
- FAD, RD7, SO4
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Trypanothione reductase (EC 1.8.1.12) | protein | 492 | 31% helix, 25% strand | Q389T8 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- RD7 · 1-[2-(piperazin-1-yl)ethyl]-5-{5-[1-(pyrrolidin-1-yl) cyclohexyl]-1,3-thiazol-2-yl}-1H-indole · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1143 | 0.84 | 0.85 | 104 | empty |
| 2 | 879 | 0.81 | 0.83 | 103 | FAD, SO4 |
| 3 | 804 | 0.80 | 0.83 | 95 | FAD, EPE |
| 4 | 624 | 0.69 | 0.78 | 62 | empty |
| 5 | 79 | 0.29 | 0.72 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 3280 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6BTL · Crystal structure of Trypanothione Reductase from Trypanosoma brucei in complex with… · 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 Q389T8
- Elsewhere: RCSB PDB 6BTL · PDBe 6BTL · UniProt Q389T8
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