Complex 9qqq

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	Electron Microscopy
Experimental resolution	2.26
System mass	2266.26 kDa
Deposition year	2025
Molecule type	RNA/Protein
# RNA entities	1
Organism	Escherichia
RCSB PDB Entry	9qqq
Reference	Wright Gerard, Cook Michael, Xu Min, Morici Martino, Travin Dmitrii, Wang Wenliang, Klepacki Dorota, Chhabra Nandini, Rao Vishwas, Sahile Henok, Hackenberger Dirk, Safdari Haaris, Berger Max, Corazza Martina, Bond Austin, Guitor Allison., Tertigas Dominique, Wang Lijun, Schaenzer Adam, Ejim Linda, Yarlagadda Venkateswarlu, Gomez James, Surette Michael, Av-Gay Yossef, Dhar Neeraj, Hung Deborah, Vázquez-Laslop Nora, Mankin Alexander, Wilson Daniel. 2025. Saskemycin, a potent and selective antimycobacterial agent targeting a unique site on the ribosome preprint (Research Square)
Equivalence Class	NR_all_56726.172 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	A1JA7
Residue	. / 1601
Chain	FB / A
Non-redundant	True
Interacting RNA chains	G/A
RNA environment detailled	protein
RNA environment global	RNA/Protein
RNA family chains	G/A: rRNA
RNA family global	rRNA
Volume	305.27 Å³
Hydrophobicity	0.204
Hydrophilicity	1.061
Buriedness	0.667
Don/acc character	1.255
SiteScore	1.044
D Score	0.885
Kd	—