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Harnessing RIBOnucleic acid - Small molecules Structures
Illustration - complex

Complex 3skl

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 2.90
System mass 46.36 kDa
Deposition year 2011
Molecule type RNA
# RNA entities 1
Organism Mesoplasma
RCSB PDB Entry 3skl
Reference Pikovskaya Olga, Polonskaia Anna, Patel Dinshaw J, Serganov Alexander. 2011. Structural principles of nucleoside selectivity in a 2′-deoxyguanosine riboswitch Nature Chemical Biology
Equivalence Class NR_all_47330.3
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 GNG
Residue . / 120
Chain C / A
Non-redundant False
Interacting RNA chains A/A
RNA environment detailled ion
RNA environment global RNA
RNA family chains A/A: riboswitch
RNA family global riboswitch
Volume 570.07 Å3
Hydrophobicity 0.126
Hydrophilicity 1.383
Buriedness 0.745
Don/acc character 0.903
SiteScore 1.181
D Score 0.936
Kd —

Compound GNG
Residue . / 120
Chain J / 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 584.47 Å3
Hydrophobicity 0.129
Hydrophilicity 1.384
Buriedness 0.759
Don/acc character 0.952
SiteScore 1.191
D Score 0.944
Kd —