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X-ray Crystallographic Structure Activity Relationship (SAR) of Casimiroin and its Analogs Bound to Human Qui Reductase 2
Analyse X-ray Crystallographic Structure Activity Relationship (SAR) of Casimiroin and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NHW
- Type
- protein
- Length
- 460 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.65
- Source
- Homo sapiens
- Molecule
- Ribosyldihydronicotinamide dehydrogenase [quinone]
- EC
- 1.10.99.2
- UniProt
- P16083
- Ligands
- FAD, ZXZ, ZN
- Pockets
- 2 · best druggability 0.78
Structure
x-ray diffraction · resolution 1.65 · 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
- ZXZ · 1,4-dimethylquinolin-2(1H)-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
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 562 | 0.78 | 0.84 | 44 | FAD, ZXZ |
| 2 | 583 | 0.76 | 0.82 | 48 | ZXZ, FAD |
Interfaces
1 interface between chains.
- A–B · 2096 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 3NHW · X-ray crystallographic structure activity relationship (sar) of casimiroin and its… · the same entry in another collection · chain A against A, TM-score 1.00
- P16083 · AlphaFold monomer V2.0 prediction for ribosyldihydronicotinamide dehydrogenase [quinone]… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 3NHW · PDBe 3NHW · UniProt P16083
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