Research workbench
X-ray structural study of quinone reductase II inhibition by compounds with micromolar to nanomolar range IC50 values
Analyse X-ray structural study of quinone reductase II inhibition by compounds with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OX2
- Type
- protein
- Length
- 460 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosyldihydronicotinamide dehydrogenase [quinone]
- EC
- 1.10.99.2
- UniProt
- P16083
- Ligands
- FAD, 79X, ZN
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ribosyldihydronicotinamide dehydrogenase [quinone] (EC 1.10.99.2) | protein | 230 | 40% helix, 16% strand | P16083 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- 79X · 2-hydroxy-8,9-dimethoxy-6H-isoindolo[2,1-a]indol-6-one · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 620 | 0.76 | 0.82 | 47 | FAD, 79X |
| 2 | 603 | 0.75 | 0.81 | 45 | 79X, FAD |
| 3 | 51 | 0.25 | 0.73 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 2040 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 3OX2 · X-ray Structural study of qui reductase II inhibition by compounds with micromolar to… · 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 P16083
- Elsewhere: RCSB PDB 3OX2 · PDBe 3OX2 · UniProt P16083
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