Complex 8hb8

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	2.30
System mass	19.46 kDa
Deposition year	2022
Molecule type	RNA
# RNA entities	1
Organism	Streptococcus
RCSB PDB Entry	8hb8
Reference	Peng Xuemei, Liao Wenjian, Lin Xiaowei, Lilley David M J, Huang Lin. 2023. Crystal structures of the NAD+-II riboswitch reveal two distinct ligand-binding pockets Nucleic Acids Research
Equivalence Class	NR_all_36913.3 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	NMN
Residue	. / 101
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	131.37 Å³
Hydrophobicity	0.554
Hydrophilicity	0.890
Buriedness	0.674
Don/acc character	3.660
SiteScore	1.007
D Score	0.854
Kd	—

Pocket 2

Compound	NMN
Residue	. / 102
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	256.91 Å³
Hydrophobicity	0.330
Hydrophilicity	1.287
Buriedness	0.653
Don/acc character	1.209
SiteScore	1.120
D Score	0.912
Kd	—