Research workbench
Synthesis of novel MT3 receptor ligands via unusual knoevenagel condensation
Analyse Synthesis of novel MT3 receptor ligands via unusual knoevenagel condensation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GQI
- 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, M49, ZN
- Pockets
- 2 · best druggability 0.77
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
- M49 · N-{(3R)-3-[2-(acetylamino)ethyl]-2-oxo-2,3-dihydro-1H-indol-5-yl}acetamide · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 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 | 571 | 0.77 | 0.83 | 47 | FAD, M49 |
| 2 | 559 | 0.76 | 0.83 | 42 | M49, FAD |
Interfaces
1 interface between chains.
- A–B · 2105 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 4GQI · Synthesis of novel MT3 receptor ligands via unusual Knoevenagel condensation · 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 4GQI · PDBe 4GQI · UniProt P16083
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