MolNFT v1 · #125046 · RNA

Selective small molecule inhibition of the FMN riboswitch

5KX9: “Selective small molecule inhibition of the FMN riboswitch”. X-ray diffraction, 3 ligands (6YG, K, MG), 5 pockets (best druggability 0.74). MolNFT v1 #125046 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5KX9
Type: RNA
Length: 108 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: FMN riboswitch
Ligands: 6YG, K, MG
Pockets: 5 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
X	FMN riboswitch	rna	52	—	—
Y	FMN riboswitch	rna	56	—	—

Ligands and binding sites

6YG · 2-[(3~{S})-1-[(2-methoxypyrimidin-5-yl) methyl]piperidin-3-yl]-6-thiophen-2-yl-1~{H}-pyrimidin-4-one · ligand · chains X, Y
K · Potassium ion · metal · 7 copies · chains X, Y
MG · Magnesium ion · metal · 4 copies · chains X, Y

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

5 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	782	0.74	0.80	39	6YG, K
2	112	0.44	0.78	15	empty
3	109	0.34	0.74	14	K
4	60	0.32	0.77	9	K
5	58	0.27	0.75	14	K

Interfaces

1 interface between chains.

X–Y · 2625 Å² buried · 167 hydrogen bonds · nucleic-nucleic

Compared structures

5KX9 · 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 5KX9 · PDBe 5KX9

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