MolNFT v1 · #117556 · protein
Trypanothione reductase in complex with 6-(sec-butoxy)-2-((3- CHLOROPHENYL)THIO)PYRIMIDIN-4-amine
5EBK: “Trypanothione reductase in complex with 6-(sec-butoxy)-2-((3- CHLOROPHENYL)THIO)PYRIMIDIN-4-amine”. X-ray diffraction, 3 ligands (RDS, FAD, SO4), 8 pockets (best druggability 0.86). MolNFT v1 #117556 on GenesisL1: 3D structure…
- PDB
- 5EBK
- Type
- protein
- Length
- 973 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trypanothione reductase
- EC
- 1.8.1.12
- UniProt
- A4HSF7
- Ligands
- RDS, FAD, SO4
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trypanothione reductase (EC 1.8.1.12) | protein | 486 | 31% helix, 27% strand | A4HSF7 |
| B | Trypanothione reductase (EC 1.8.1.12) | protein | 487 | 31% helix, 26% strand | A4HSF7 |
Ligands and binding sites
- RDS · 6-sec-Butoxy-2-[(3-chlorophenyl)sulfanyl]-4-pyrimidinamine · ligand · 7 copies · chains A, B
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 887 | 0.86 | 0.88 | 86 | RDS |
| 2 | 360 | 0.82 | 0.91 | 59 | FAD |
| 3 | 767 | 0.79 | 0.83 | 94 | FAD, RDS, SO4 |
| 4 | 429 | 0.61 | 0.76 | 49 | RDS |
| 5 | 230 | 0.59 | 0.80 | 38 | RDS |
Interfaces
1 interface between chains.
- A–B · 3271 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5EBK · Trypanothione reductase in complex with 6-(sec-butoxy)-2-((3-chlorophenyl)thio)pyrimidin-4… · 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 A4HSF7
- Elsewhere: RCSB PDB 5EBK · PDBe 5EBK · UniProt A4HSF7
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