Research workbench
Trypanosoma brucei trypanothione reductase in complex with 3,4- dihydroquinazoline inhibitor (DDD00085762)
Analyse Trypanosoma brucei trypanothione reductase in complex with 3,4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WPF
- Type
- protein
- Length
- 1,955 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trypanothione reductase
- EC
- 1.8.1.12
- UniProt
- P39051
- Ligands
- FAD, WPF, CL, BR
- Pockets
- 14 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trypanothione reductase (EC 1.8.1.12) | protein | 490 | 33% helix, 28% strand | P39051 |
| B | Trypanothione reductase (EC 1.8.1.12) | protein | 487 | 34% helix, 28% strand | P39051 |
| C | Trypanothione reductase (EC 1.8.1.12) | protein | 487 | 34% helix, 28% strand | P39051 |
| D | Trypanothione reductase (EC 1.8.1.12) | protein | 491 | 33% helix, 27% strand | P39051 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- WPF · 3-[(4S)-6-chloro-2-methyl-4-(4-methylphenyl)quinazolin-3(4H)-yl]-N,N-dimethylpropan-1-amine · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 7 copies · chains A, B, C
- BR · Bromide ion · ion · 3 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 990 | 0.87 | 0.88 | 100 | WPF |
| 2 | 970 | 0.87 | 0.88 | 104 | WPF |
| 3 | 766 | 0.80 | 0.83 | 96 | FAD, CL |
| 4 | 773 | 0.79 | 0.83 | 98 | FAD, CL |
| 5 | 661 | 0.79 | 0.84 | 93 | FAD, CL |
Interfaces
3 interfaces between chains.
- A–B · 3400 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 3369 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 81 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 2WPF · Trypanosoma brucei trypanothione reductase in complex with 3,4- dihydroquinazoline… · the same entry in another collection · chain C against C, TM-score 1.00
- P39051 · AlphaFold monomer V2.0 prediction for trypanothione reductase (P39051) · a predicted model of the same protein · chain B 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 P39051
- Elsewhere: RCSB PDB 2WPF · PDBe 2WPF · UniProt P39051
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