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Harnessing RIBOnucleic acid - Small molecules Structures
Illustration - complex

Complex 6dmc

Legend

Pocket colors by molecule type

 RNA

 Protein

 DNA

These colors appear when a pocket is selected (the structure fades to show the pocket surface). Colors from the molecule-type palette (RNA / protein / DNA).

System information

Experimental technique X-ray
Experimental resolution 2.20
System mass 68.62 kDa
Deposition year 2018
Molecule type RNA
# RNA entities 1
Organism Sulfobacillus
RCSB PDB Entry 6dmc
Reference Peselis Alla, Serganov Alexander. 2018. ykkC riboswitches employ an add-on helix to adjust specificity for polyanionic ligands Nature Chemical Biology
Equivalence Class NR_all_86427.3
BGSU version: 4.52

Pockets List

Legend

Cell colors for SiteScore and D Score:

 Favourable

 Intermediate

 Unfavourable

 Not available

ScoreThresholdMeaning
SiteScore< 0.8Non-drug binding site
SiteScore0.8 – 1.0Potential drug binding site
SiteScore> 1.0Promising binding site
D Score< 0.83Undruggable
D Score0.83 – 0.98Difficult
D Score> 0.98Druggable

Tick a pocket below to highlight it in the 3D structure above.

Compound G4P
Residue . / 201
Chain C / A
Non-redundant True
Interacting RNA chains A/A
RNA environment detailled ion
RNA environment global RNA
RNA family chains A/A: riboswitch
RNA family global riboswitch
Volume 282.29 Å3
Hydrophobicity 0.179
Hydrophilicity 1.094
Buriedness 0.625
Don/acc character 1.155
SiteScore 1.071
D Score 0.920
Kd 0.51uM

Compound G4P
Residue . / 201
Chain W / B
Non-redundant False
Interacting RNA chains B/B
RNA environment detailled ion
RNA environment global RNA
RNA family chains B/B: riboswitch
RNA family global riboswitch
Volume 488.78 Å3
Hydrophobicity 0.181
Hydrophilicity 1.032
Buriedness 0.638
Don/acc character 1.455
SiteScore 1.112
D Score 0.987
Kd 0.51uM