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Harnessing RIBOnucleic acid - Small molecules Structures

Illustration - complex

Complex 9sum

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 1.99
System mass 3102.80 kDa
Deposition year 2025
Molecule type RNA/Protein
# RNA entities 1
Organism Candidozyma
RCSB PDB Entry 9sum
Reference Atamas Anastasia, Stetsenko Artem, Incarnato Danny, Valero Alicia Maciá, Rogachev Andrey, Billerbeck Sonja, Guskov Albert. 2026. Unveiling the molecular architecture of Candida auris ribosome Structure
Equivalence Class NR_all_03090.1, NR_all_36496.1, NR_all_54471.1
BGSU version: 4.56

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 3HE
Residue . / 3469
Chain MI / A
Non-redundant True
Interacting RNA chains C/A
RNA environment detailled protein, other
RNA environment global RNA/Other
RNA family chains C/A: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 3301
Chain AC / A
Non-redundant True
Interacting RNA chains C/A, E/C
RNA environment detailled protein
RNA environment global RNA/Protein
RNA family chains C/A: rRNA, E/C: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 3471
Chain OI / A
Non-redundant True
Interacting RNA chains C/A, E/C
RNA environment detailled protein, ion
RNA environment global RNA/Protein
RNA family chains C/A: rRNA, E/C: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 3472
Chain PI / A
Non-redundant True
Interacting RNA chains C/A, E/C
RNA environment detailled protein
RNA environment global RNA/Protein
RNA family chains C/A: rRNA, E/C: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 3473
Chain QI / A
Non-redundant True
Interacting RNA chains C/A
RNA environment detailled protein
RNA environment global RNA/Protein
RNA family chains C/A: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 3474
Chain RI / A
Non-redundant True
Interacting RNA chains C/A
RNA environment detailled protein
RNA environment global RNA/Protein
RNA family chains C/A: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 3475
Chain SI / A
Non-redundant True
Interacting RNA chains C/A
RNA environment detailled protein
RNA environment global RNA/Protein
RNA family chains C/A: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 3476
Chain TI / A
Non-redundant True
Interacting RNA chains C/A
RNA environment detailled RNA-only
RNA environment global RNA
RNA family chains C/A: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 3477
Chain UI / A
Non-redundant True
Interacting RNA chains C/A
RNA environment detailled protein, other
RNA environment global RNA/Other
RNA family chains C/A: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 3478
Chain VI / A
Non-redundant True
Interacting RNA chains C/A
RNA environment detailled protein
RNA environment global RNA/Protein
RNA family chains C/A: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 3479
Chain WI / A
Non-redundant True
Interacting RNA chains C/A
RNA environment detailled protein
RNA environment global RNA/Protein
RNA family chains C/A: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 3480
Chain XI / A
Non-redundant True
Interacting RNA chains C/A
RNA environment detailled protein
RNA environment global RNA/Protein
RNA family chains C/A: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 3481
Chain YI / A
Non-redundant True
Interacting RNA chains C/A
RNA environment detailled protein
RNA environment global RNA/Protein
RNA family chains C/A: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 3482
Chain ZI / A
Non-redundant True
Interacting RNA chains C/A
RNA environment detailled RNA-only
RNA environment global RNA
RNA family chains C/A: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 3483
Chain AJ / A
Non-redundant True
Interacting RNA chains C/A
RNA environment detailled protein, ion
RNA environment global RNA/Protein
RNA family chains C/A: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 3484
Chain BJ / A
Non-redundant True
Interacting RNA chains C/A
RNA environment detailled ion
RNA environment global RNA
RNA family chains C/A: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 3485
Chain CJ / A
Non-redundant True
Interacting RNA chains C/A
RNA environment detailled protein, other
RNA environment global RNA/Other
RNA family chains C/A: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 3486
Chain DJ / A
Non-redundant True
Interacting RNA chains C/A
RNA environment detailled other
RNA environment global RNA/Other
RNA family chains C/A: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 3487
Chain EJ / A
Non-redundant True
Interacting RNA chains C/A
RNA environment detailled protein
RNA environment global RNA/Protein
RNA family chains C/A: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 3488
Chain FJ / A
Non-redundant True
Interacting RNA chains D/B, C/A
RNA environment detailled protein
RNA environment global RNA/Protein
RNA family chains C/A: rRNA, D/B: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 3489
Chain GJ / A
Non-redundant True
Interacting RNA chains C/A
RNA environment detailled protein, other
RNA environment global RNA/Other
RNA family chains C/A: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 3490
Chain HJ / A
Non-redundant True
Interacting RNA chains C/A
RNA environment detailled RNA-only
RNA environment global RNA
RNA family chains C/A: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 3491
Chain IJ / A
Non-redundant True
Interacting RNA chains C/A
RNA environment detailled protein
RNA environment global RNA/Protein
RNA family chains C/A: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 3492
Chain JJ / A
Non-redundant True
Interacting RNA chains C/A
RNA environment detailled protein, ion
RNA environment global RNA/Protein
RNA family chains C/A: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 3493
Chain KJ / A
Non-redundant True
Interacting RNA chains C/A
RNA environment detailled RNA-only
RNA environment global RNA
RNA family chains C/A: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 3494
Chain LJ / A
Non-redundant True
Interacting RNA chains C/A
RNA environment detailled RNA-only
RNA environment global RNA
RNA family chains C/A: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 3495
Chain MJ / A
Non-redundant True
Interacting RNA chains C/A
RNA environment detailled protein
RNA environment global RNA/Protein
RNA family chains C/A: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 3496
Chain NJ / A
Non-redundant True
Interacting RNA chains C/A
RNA environment detailled ion
RNA environment global RNA
RNA family chains C/A: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 3497
Chain OJ / A
Non-redundant True
Interacting RNA chains C/A
RNA environment detailled protein
RNA environment global RNA/Protein
RNA family chains C/A: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 3498
Chain PJ / A
Non-redundant True
Interacting RNA chains C/A
RNA environment detailled RNA-only
RNA environment global RNA
RNA family chains C/A: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 3499
Chain QJ / A
Non-redundant True
Interacting RNA chains C/A
RNA environment detailled RNA-only
RNA environment global RNA
RNA family chains C/A: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 3500
Chain RJ / A
Non-redundant True
Interacting RNA chains C/A
RNA environment detailled protein
RNA environment global RNA/Protein
RNA family chains C/A: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 203
Chain UJ / B
Non-redundant True
Interacting RNA chains D/B
RNA environment detailled protein
RNA environment global RNA/Protein
RNA family chains D/B: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 203
Chain XJ / C
Non-redundant True
Interacting RNA chains E/C
RNA environment detailled protein
RNA environment global RNA/Protein
RNA family chains E/C: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 204
Chain YJ / C
Non-redundant True
Interacting RNA chains E/C
RNA environment detailled protein
RNA environment global RNA/Protein
RNA family chains E/C: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 205
Chain ZJ / C
Non-redundant True
Interacting RNA chains E/C
RNA environment detailled protein
RNA environment global RNA/Protein
RNA family chains E/C: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 206
Chain AK / C
Non-redundant True
Interacting RNA chains C/A, E/C
RNA environment detailled RNA-only
RNA environment global RNA
RNA family chains C/A: rRNA, E/C: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 1874
Chain WM / CA
Non-redundant True
Interacting RNA chains F/CA
RNA environment detailled RNA-only
RNA environment global RNA
RNA family chains F/CA: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 1875
Chain XM / CA
Non-redundant True
Interacting RNA chains F/CA
RNA environment detailled protein, ion
RNA environment global RNA/Protein
RNA family chains F/CA: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 1876
Chain YM / CA
Non-redundant True
Interacting RNA chains F/CA
RNA environment detailled protein
RNA environment global RNA/Protein
RNA family chains F/CA: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 1877
Chain ZM / CA
Non-redundant True
Interacting RNA chains F/CA
RNA environment detailled protein
RNA environment global RNA/Protein
RNA family chains F/CA: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 1878
Chain AN / CA
Non-redundant True
Interacting RNA chains F/CA
RNA environment detailled RNA-only
RNA environment global RNA
RNA family chains F/CA: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 1879
Chain BN / CA
Non-redundant True
Interacting RNA chains F/CA
RNA environment detailled protein
RNA environment global RNA/Protein
RNA family chains F/CA: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 1880
Chain CN / CA
Non-redundant True
Interacting RNA chains F/CA
RNA environment detailled protein
RNA environment global RNA/Protein
RNA family chains F/CA: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 1882
Chain EN / CA
Non-redundant True
Interacting RNA chains F/CA
RNA environment detailled RNA-only
RNA environment global RNA
RNA family chains F/CA: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 1883
Chain FN / CA
Non-redundant True
Interacting RNA chains F/CA
RNA environment detailled other
RNA environment global RNA/Other
RNA family chains F/CA: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 1884
Chain GN / CA
Non-redundant True
Interacting RNA chains F/CA
RNA environment detailled protein
RNA environment global RNA/Protein
RNA family chains F/CA: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 1885
Chain HN / CA
Non-redundant True
Interacting RNA chains F/CA
RNA environment detailled protein
RNA environment global RNA/Protein
RNA family chains F/CA: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 1886
Chain IN / CA
Non-redundant True
Interacting RNA chains F/CA
RNA environment detailled protein
RNA environment global RNA/Protein
RNA family chains F/CA: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 1887
Chain JN / CA
Non-redundant True
Interacting RNA chains F/CA
RNA environment detailled protein
RNA environment global RNA/Protein
RNA family chains F/CA: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 1888
Chain KN / CA
Non-redundant True
Interacting RNA chains F/CA
RNA environment detailled protein, ion
RNA environment global RNA/Protein
RNA family chains F/CA: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 1889
Chain LN / CA
Non-redundant True
Interacting RNA chains F/CA
RNA environment detailled protein
RNA environment global RNA/Protein
RNA family chains F/CA: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 1890
Chain MN / CA
Non-redundant True
Interacting RNA chains F/CA
RNA environment detailled protein
RNA environment global RNA/Protein
RNA family chains F/CA: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 1891
Chain NN / CA
Non-redundant True
Interacting RNA chains F/CA
RNA environment detailled protein
RNA environment global RNA/Protein
RNA family chains F/CA: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 1892
Chain ON / CA
Non-redundant True
Interacting RNA chains F/CA
RNA environment detailled protein
RNA environment global RNA/Protein
RNA family chains F/CA: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 1893
Chain PN / CA
Non-redundant True
Interacting RNA chains F/CA
RNA environment detailled protein, ion, other
RNA environment global RNA/Other
RNA family chains F/CA: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 402
Chain RN / E
Non-redundant True
Interacting RNA chains C/A
RNA environment detailled protein
RNA environment global RNA/Protein
RNA family chains C/A: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —

Compound GET
Residue . / 301
Chain VN / T
Non-redundant True
Interacting RNA chains C/A
RNA environment detailled protein
RNA environment global RNA/Protein
RNA family chains C/A: rRNA
RNA family global rRNA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -
Kd —