MolNFT v1 · #114919 · RNA
Selective small molecule inhibition of the FMN riboswitch
5C45: “Selective small molecule inhibition of the FMN riboswitch”. X-ray diffraction, 3 ligands (51B, K, MG), 6 pockets (best druggability 0.75). MolNFT v1 #114919 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5C45
- Type
- RNA
- Length
- 109 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FMN riboswitch
- Ligands
- 51B, K, MG
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X | FMN riboswitch | rna | 53 | — | — |
| Y | FMN riboswitch | rna | 56 | — | — |
Ligands and binding sites
- 51B · 2-[(3S)-1-{[2-(methylamino)pyrimidin-5-yl]methyl}piperidin-3-yl]-6-(thiophen-2-yl)pyrimidin-4(1H)-one · ligand · chains X, Y
- K · Potassium ion · metal · 6 copies · chains X, Y
- MG · Magnesium ion · metal · 2 copies · chains X, Y
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 772 | 0.75 | 0.80 | 38 | 51B, K |
| 2 | 124 | 0.44 | 0.78 | 15 | empty |
| 3 | 100 | 0.33 | 0.74 | 11 | empty |
| 4 | 52 | 0.32 | 0.78 | 8 | K |
| 5 | 60 | 0.31 | 0.77 | 14 | MG |
Interfaces
1 interface between chains.
- X–Y · 2641 Ų buried · 180 hydrogen bonds · nucleic-nucleic
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 5C45 · PDBe 5C45
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