HARIBOSS logo

HARIBOSS

Harnessing RIBOnucleic acid - Small molecules Structures
Illustration - complex

Complex 9pj7

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 2.40
System mass 2282.41 kDa
Deposition year 2025
Molecule type RNA/Protein
# RNA entities 1
Organism Cutibacterium
RCSB PDB Entry 9pj7
Reference Devarkar Swapnil C., Lomakin Ivan B., Wang Jimin, Grada Ayman, Bunick Christopher G.. 2026. Dual site targeting of the bacterial 70S ribosome by tetracyclines Nature Communications
Equivalence Class NR_all_00194.1, NR_all_86966.1
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 DXT
Residue . / 1615
Chain TB / A
Non-redundant True
Interacting RNA chains CA/Y, F/A
RNA environment detailled ion
RNA environment global RNA
RNA family chains F/A: rRNA, CA/Y: mRNA
RNA family global multiple
Volume 175.62 Å3
Hydrophobicity 0.397
Hydrophilicity 1.026
Buriedness 0.752
Don/acc character 2.358
SiteScore 0.948
D Score 0.747
Kd —

Compound DXT
Residue . / 3123
Chain CE / a
Non-redundant True
Interacting RNA chains DA/a
RNA environment detailled ion
RNA environment global RNA
RNA family chains DA/a: rRNA
RNA family global rRNA
Volume 756.66 Å3
Hydrophobicity 0.276
Hydrophilicity 0.884
Buriedness 0.712
Don/acc character 3.465
SiteScore 1.189
D Score 1.079
Kd —

Compound DXT
Residue . / 3130
Chain JE / a
Non-redundant True
Interacting RNA chains DA/a
RNA environment detailled ion, other
RNA environment global RNA/Other
RNA family chains DA/a: rRNA
RNA family global rRNA
Volume 458.25 Å3
Hydrophobicity 0.857
Hydrophilicity 0.755
Buriedness 0.768
Don/acc character 3.590
SiteScore 1.105
D Score 0.967
Kd —

Compound DXT
Residue . / 3138
Chain RE / a
Non-redundant True
Interacting RNA chains DA/a
RNA environment detailled ion, other
RNA environment global RNA/Other
RNA family chains DA/a: rRNA
RNA family global rRNA
Volume 387.25 Å3
Hydrophobicity 0.546
Hydrophilicity 1.129
Buriedness 0.787
Don/acc character 1.719
SiteScore 1.067
D Score 0.862
Kd —

Compound DXT
Residue . / 3146
Chain ZE / a
Non-redundant True
Interacting RNA chains DA/a
RNA environment detailled ion, other
RNA environment global RNA/Other
RNA family chains DA/a: rRNA
RNA family global rRNA
Volume 610.54 Å3
Hydrophobicity 0.786
Hydrophilicity 0.847
Buriedness 0.766
Don/acc character 2.511
SiteScore 1.233
D Score 1.123
Kd —

Compound DXT
Residue . / 201
Chain MM / r
Non-redundant True
Interacting RNA chains DA/a
RNA environment detailled protein, ion, other
RNA environment global RNA/Other
RNA family chains DA/a: rRNA
RNA family global rRNA
Volume 661.65 Å3
Hydrophobicity 0.288
Hydrophilicity 1.301
Buriedness 0.773
Don/acc character 1.178
SiteScore 1.200
D Score 0.980
Kd —

Compound DXT
Residue . / 201
Chain NM / s
Non-redundant True
Interacting RNA chains DA/a
RNA environment detailled protein, ion, other
RNA environment global RNA/Other
RNA family chains DA/a: rRNA
RNA family global rRNA
Volume 136.86 Å3
Hydrophobicity 0.013
Hydrophilicity 1.112
Buriedness 0.761
Don/acc character 2.018
SiteScore 0.770
D Score 0.493
Kd —