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Harnessing RIBOnucleic acid - Small molecules Structures
Illustration - complex

Complex 4f8u

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 2.00
System mass 14.69 kDa
Deposition year 2012
Molecule type RNA
# RNA entities 1
Organism N/A
RCSB PDB Entry 4f8u
Reference Kondo Jiro, Koganei Mai, Kasahara Tomoko. 2012. Crystal Structure and Specific Binding Mode of Sisomicin to the Bacterial Ribosomal Decoding Site ACS Medicinal Chemistry Letters
Equivalence Class NR_all_71199.7
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 SIS
Residue . / 101
Chain C / A
Non-redundant True
Interacting RNA chains B/B, A/A
RNA environment detailled RNA-only
RNA environment global RNA
RNA family chains A/A: rRNA, B/B: rRNA
RNA family global rRNA
Volume 115.93 Å3
Hydrophobicity 0.104
Hydrophilicity 0.736
Buriedness 0.550
Don/acc character 4.675
SiteScore 0.857
D Score 0.706
Kd —

Compound SIS
Residue . / 101
Chain D / B
Non-redundant True
Interacting RNA chains B/B, A/A
RNA environment detailled RNA-only
RNA environment global RNA
RNA family chains A/A: rRNA, B/B: rRNA
RNA family global rRNA
Volume 51.79 Å3
Hydrophobicity 0.256
Hydrophilicity 0.736
Buriedness 0.536
Don/acc character 2.865
SiteScore 0.788
D Score 0.622
Kd —