Research workbench

Selective small molecule inhibition of the FMN riboswitch

Analyse Selective small molecule inhibition of the FMN riboswitch in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

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.

Pocket	Volume (Å³)	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 Å² buried · 180 hydrogen bonds · nucleic-nucleic

Compared structures

5C45 · Selective Small Molecule Inhibition of the FMN Riboswitch · the same entry in another collection · chain X against X, 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
Elsewhere: RCSB PDB 5C45 · PDBe 5C45

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.