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Harnessing RIBOnucleic acid - Small molecules Structures
Illustration - complex

Complex 4lvy

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 2.00
System mass 29.70 kDa
Deposition year 2013
Molecule type RNA
# RNA entities 1
Organism Streptococcus
RCSB PDB Entry 4lvy
Reference Trausch Jeremiah J., Batey Robert T.. 2014. A Disconnect between High-Affinity Binding and Efficient Regulation by Antifolates and Purines in the Tetrahydrofolate Riboswitch Chemistry & Biology
Equivalence Class NR_all_78797.7
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 LYA
Residue . / 101
Chain B / A
Non-redundant True
Interacting RNA chains A/A
RNA environment detailled RNA-only
RNA environment global RNA
RNA family chains A/A: riboswitch
RNA family global riboswitch
Volume 81.63 Å3
Hydrophobicity 0.103
Hydrophilicity 0.900
Buriedness 0.584
Don/acc character 3.630
SiteScore 0.712
D Score 0.498
Kd 110uM

Compound LYA
Residue . / 102
Chain C / A
Non-redundant True
Interacting RNA chains A/A
RNA environment detailled RNA-only
RNA environment global RNA
RNA family chains A/A: riboswitch
RNA family global riboswitch
Volume 103.24 Å3
Hydrophobicity 0.090
Hydrophilicity 0.924
Buriedness 0.637
Don/acc character 1.028
SiteScore 0.765
D Score 0.551
Kd 110uM