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Harnessing RIBOnucleic acid - Small molecules Structures
Illustration - complex

Complex 3slm

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 2.70
System mass 46.17 kDa
Deposition year 2011
Molecule type RNA
# RNA entities 1
Organism Mesoplasma
RCSB PDB Entry 3slm
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_21705.3
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 DGP
Residue . / 120
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 605.40 Å3
Hydrophobicity 0.062
Hydrophilicity 1.362
Buriedness 0.752
Don/acc character 0.957
SiteScore 1.186
D Score 0.947
Kd 379uM

Compound DGP
Residue . / 120
Chain L / 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 519.30 Å3
Hydrophobicity 0.119
Hydrophilicity 1.342
Buriedness 0.747
Don/acc character 1.046
SiteScore 1.183
D Score 0.951
Kd 379uM