Complex 3d2x

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	2.50
System mass	51.09 kDa
Deposition year	2008
Molecule type	RNA
# RNA entities	1
Organism	Arabidopsis
RCSB PDB Entry	3d2x
Reference	Thore Stéphane, Frick Christian, Ban Nenad. 2008. Structural Basis of Thiamine Pyrophosphate Analogues Binding to the Eukaryotic Riboswitch Journal of the American Chemical Society
Equivalence Class	NR_all_27756.3 BGSU version: 4.52

Pockets List

Legend

Cell colors for SiteScore and D Score:

Favourable

Intermediate

Unfavourable

Not available

Score	Threshold	Meaning
SiteScore	< 0.8	Non-drug binding site
SiteScore	0.8 – 1.0	Potential drug binding site
SiteScore	> 1.0	Promising binding site
D Score	< 0.83	Undruggable
D Score	0.83 – 0.98	Difficult
D Score	> 0.98	Druggable

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

Pocket 1

Compound	D2X
Residue	. / 85
Chain	J / 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	292.92 Å³
Hydrophobicity	0.590
Hydrophilicity	0.941
Buriedness	0.787
Don/acc character	2.766
SiteScore	0.946
D Score	0.752
Kd	—

Pocket 2

Compound	D2X
Residue	. / 84
Chain	Q / 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	775.87 Å³
Hydrophobicity	0.232
Hydrophilicity	1.141
Buriedness	0.740
Don/acc character	1.513
SiteScore	1.178
D Score	1.012
Kd	—