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Harnessing RIBOnucleic acid - Small molecules Structures
Illustration - complex

Complex 4qln

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 2.65
System mass 41.88 kDa
Deposition year 2014
Molecule type RNA
# RNA entities 1
Organism Caldanaerobacter
RCSB PDB Entry 4qln
Reference Ren Aiming, Patel Dinshaw J. 2014. c-di-AMP binds the ydaO riboswitch in two pseudo-symmetry–related pockets Nature Chemical Biology
Equivalence Class NR_all_53735.3
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 2BA
Residue . / 201
Chain B / 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 404.74 Å3
Hydrophobicity 0.562
Hydrophilicity 0.910
Buriedness 0.721
Don/acc character 1.443
SiteScore 1.191
D Score 1.076
Kd 2.9uM

Compound 2BA
Residue . / 202
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 430.47 Å3
Hydrophobicity 0.245
Hydrophilicity 0.920
Buriedness 0.701
Don/acc character 1.260
SiteScore 1.164
D Score 1.047
Kd 2.9uM