MolNFT v1 · #28357 · protein
Structure of trihydroxynaphthalene reductase in complex with NADPH and an active site inhibitor
1YBV: “Structure of trihydroxynaphthalene reductase in complex with NADPH and an active site inhibitor”. X-ray diffraction, 2 ligands (NDP, BEA), 5 pockets (best druggability 0.78). MolNFT v1 #28357 on GenesisL1: 3D structure, binding…
- PDB
- 1YBV
- Type
- protein
- Length
- 540 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trihydroxynaphthalene reductase
- EC
- 1.3.1.50
- UniProt
- Q12634
- Ligands
- NDP, BEA
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Trihydroxynaphthalene reductase (EC 1.3.1.50) | protein | 270 | 50% helix, 15% strand | Q12634 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- BEA · 5-methyl-1,2,4-triazolo[3,4-b]benzothiazole · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 385 | 0.78 | 0.87 | 43 | NDP, BEA |
| 2 | 399 | 0.77 | 0.86 | 43 | NDP, BEA |
| 3 | 448 | 0.62 | 0.76 | 46 | empty |
| 4 | 85 | 0.38 | 0.77 | 15 | empty |
| 5 | 71 | 0.37 | 0.78 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 2062 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 1YBV · Structure of trihydroxynaphthalene reductase in complex with NADPH and an active site… · the same entry in another collection · chain A against A, TM-score 1.00
- Q12634 · AlphaFold monomer V2.0 prediction for tetrahydroxynaphthalene reductase (Q12634) · a predicted model of the same protein · 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 Q12634
- Elsewhere: RCSB PDB 1YBV · PDBe 1YBV · UniProt Q12634
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