MolNFT v1 · #53269 · protein
Trypanosoma brucei trypanothione reductase in complex with 3,4-dihydroquinazoline inhibitor (DDD00073359)
2WPE: “Trypanosoma brucei trypanothione reductase in complex with 3,4-dihydroquinazoline inhibitor (DDD00073359)”. X-ray diffraction, 4 ligands (FAD, WPE, NA), 11 pockets (best druggability 0.87). MolNFT v1 #53269 on GenesisL1: 3D…
- PDB
- 2WPE
- Type
- protein
- Length
- 1,949 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trypanothione reductase
- EC
- 1.8.1.12
- UniProt
- Q389T8
- Ligands
- FAD, WPE, NA, CL
- Pockets
- 11 · 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 | 34% helix, 28% strand | Q389T8 |
| B | Trypanothione reductase (EC 1.8.1.12) | protein | 486 | 34% helix, 28% strand | Q389T8 |
| C | Trypanothione reductase (EC 1.8.1.12) | protein | 484 | 33% helix, 28% strand | Q389T8 |
| D | Trypanothione reductase (EC 1.8.1.12) | protein | 489 | 33% helix, 28% strand | Q389T8 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- WPE · N-{2-[(4S)-6-chloro-2-methyl-4-phenylquinazolin-3(4H)-yl]ethyl}furan-2-carboxamide · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 18 copies · chains A, B, C, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
- MRD · (4R)-2-methylpentane-2,4-diol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1006 | 0.87 | 0.88 | 100 | NA, CL, WPE |
| 2 | 1083 | 0.87 | 0.87 | 114 | WPE, NA, CL |
| 3 | 788 | 0.80 | 0.83 | 103 | FAD, CL |
| 4 | 810 | 0.80 | 0.83 | 102 | FAD, CL |
| 5 | 766 | 0.80 | 0.83 | 97 | FAD, CL |
Interfaces
3 interfaces between chains.
- A–B · 3422 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 3388 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 78 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2WPE · Trypanosoma brucei trypanothione reductase in complex with 3,4- dihydroquinazoline… · the same entry in another collection · chain B against B, 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 2WPE · PDBe 2WPE · UniProt Q389T8
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