HARIBOSS

Harnessing RIBOnucleic acid - Small molecules Structures

Compounds
RNA-SM complexes
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Complexes

Complexes

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System Properties

Experimental technique Experimental resolution Molecular weight Deposition date Molecule type Organism With MD simulation With equivalence class

Ligand Properties

Molecular weight Number of atoms Number of PDB entries Lipinski rule of 5 Veber Pfizer 3/75

Pocket Properties

Number of interacting chains Pocket size SiteScore Dscore Exposure Enclosure Hydrophobicity Hydrophilicity Donor/Acceptor Volume RNA environment global RNA environment detailed RNA family global RNA family chains With binding affinity values Only one non-redundant filter can be selected at a time Non-redundant only Non-redundant only (RNA)

927 Complexes found

Complexes per page

60 120 180

filters used: RNA family global: rRNA

9rot

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Assembly intermediate of human mitochondrial ribosome small subunit bound to METTL15, RBFA, and mtIF2 (State M2.1)

9rov

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Assembly intermediate of human mitochondrial ribosome small subunit bound to METTL15 and RBFA (Inward conformation) (State M2)

9rpf

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Assembly intermediate of human mitochondrial ribosome small subunit bound to METTL15 and mS37 (State M4)

SM: NAD

9rpv

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Structure of the ZAK-bound human disome

SM: ANM

9rtu

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Structure of the 70S-EF-G(P610L)-GDP-Pi ribosome complex with tRNAs in hybrid state 1 (H1-EF-G(P610L)-GDP-Pi)

9rtv

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Structure of the 70S-EF-G(P610L)-GDP-Pi ribosome complex with tRNAs in hybrid state 2 (H2-EF-G(P610L)-GDP-Pi)

9ru6

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Human mitoribosome bound to TACO1 (Translational activator of COX1), mRNA, A/A-, P/P- and (partial) E/E-tRNAs

SM: NAD

9ru9

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RPS26dC HEK mutant 80S ribosome bound to Kozak mRNA (RPS26dC-Kozak)

9slg

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Doxycycline Bound E. coli Ribosome with Rearranged Peptidyl Transferase Centre

SM: DXT

9sx2

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30S Doxycycline Bound E. coli Ribosome

SM: DXT

9t5x

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Structure of a stalled E. coli 70S RNC-NuoK-70 in complex with the membrane protein insertase SecYEG-YidC

SM: SPM

9t61

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Doxycycline Bound C. burnetii 30S Ribosome

SM: DXT

9t6h

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Cryo-EM structure of the 70S ribosome from Francisella tularensis bound to antibiotics chloramphenicol and gentamicin

9tey

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DalDro bound to the terminating Escherichia coli 70S ribosome

SM: SPM

9tez

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DalDroS bound to the Escherichia coli 50S ribosomal subunit

SM: SPM

9ti8

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Staphylococcus aureus 50S ribosome in complex with RRF, EF-G and fusidic acid (50S-RRF-EF-G-FA)

9ti9

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Staphylococcus aureus 70S ribosome in complex with RRF, EF-G and fusidic acid (70S-RRF-EF-G-FA)

9tmi

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E. coli 70S ribosome with A- and P-site tRNA

SM: SCM

9tnl

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E. coli 70S ribosome with A/P- and P/E-site tRNA

SM: SCM

9tqa

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E. coli 70S ribosome, trapped conformational ground state of SSU-h44 apical loop, with A- and P-site tRNA

SM: SCM

9tz5

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Triple Stack Doxycycline Bound 50S Subunit of the Coxiella burnetii Ribosome

SM: DXT

9tze

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70S Coxiella burnetii Ribosome with Doxycycline and HPFcold

SM: DXT

9uwh

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human mitoribosome trapped by retapamulin

9v26

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Cryo- EM structure of 75S ribosome with A/P- & P/E- tRNAs from Entamoeba histolytica bound to antibiotic paromomycin

SM: PAR

9v29

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Cryo- EM structure of small subunit (body) of 75S ribosome with A/P- & P/E- tRNAs from Entamoeba histolytica bound to antibiotic paromomycin

SM: PAR

9vxm

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Human mitoribosome in a non-rotated state, with multiple neomycin molecules bound, featuring A/A-site and P/P-site tRNAs

SM: NAD NMY SPM

9vxn

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Human cytosolic ribosome in a rotated state, with multiple neomycin molecules bound, featuring A/P-site and P/E-site tRNAs

SM: NMY

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Experimental method

Experimental resolution

Select cutoff values for experimental resolution (Å)

Current selection range: to

Molecular Weight

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Current selection range: to

Deposition date

Select cutoff values for the deposition date (years) of the PDB entries

Current selection range: to

Molecular composition of the system

RNA

RNA/DNA/Protein

RNA/Protein

Source organism

Acinetobacter

Arabidopsis

Bacillus

Betacoronavirus

Bos

Brassica

Caenorhabditis

Candida

Chlamydomonas

Coxiella

Cutibacterium

Deinococcus

Entamoeba

Enterococcus

Enterovirus

Escherichia

Francisella

Giardia

Haloarcula

Hepacivirus

Homo

Kluyveromyces

Leishmania

Listeria

Mus

Mycobacterium

Mycolicibacterium

Mycoplasmoides

Neurospora

Nicotiana

Oryctolagus

Plasmodium

Porphyromonas

Pyrobaculum

Saccharolobus

Saccharomyces

Solanum

Staphylococcus

Streptomyces

Sulfolobus

Sus

Tequatrovirus

Thermochaetoides

Thermus

Triticum

Trypanosoma

Vibrio

Molecular weight

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Number of atoms

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Number of PDB entries

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Number of interacting chains

Select cutoff values for the number of interacting RNA chains in the pockets

Current selection range: to

Pocket size

Select cutoff values for the number of heavy RNA atoms in the pocket

Current selection range: to

SiteScore

Select cutoff values for the SiteScore, ligandability score calcultated by Schrödinger tool. Below 0.8 the pocket is considered non-drug binding site, between 0.8 and 1.0 a potential drug binding site, and above 1.0 a promising binding site [TODO add ref]

Current selection range: to

Dscore

Select cutoff values for the Dscore, druggability score calcultated by Schrödinger tool. Below 0.83 the pocket is considered undraggable, between 0.83 and 0.98 difficult, and above 0.98 druggable [TODO add ref]

Current selection range: to

Exposure

Select cutoff values for the exposure, a score calculated by Schrödinger tool which indicates the degree of exposure to the solvent of the pocket (AU)

Current selection range: to

Enclosure

Select cutoff values for the enclosure, a score calculated by Schrödinger tool which indicates the degree of buriedness of the pocket (AU)

Current selection range: to

Hydrophobicity

Select cutoff values for the hydrophobicity, a score calculated by Schrödinger tool which indicates the degree of hydrophobicity of the pocket (AU)

Current selection range: to

Hydrophilicity

Select cutoff values for the hydrophilicity, a score calculated by Schrödinger tool which indicates the degree of hydrophilicity of the pocket (AU)

Current selection range: to

Donor/Acceptor

Select cutoff values for Donor/Acceptor character of the pocket calculated by Schrödinger tool

Current selection range: to

Volume

Select cutoff values for volume of the pocket calculated by Schrödinger tool (Å³)

Current selection range: to

RNA environment global

RNA

RNA/DNA

RNA/DNA/Protein

RNA/Other

RNA/Protein

RNA environment detailed

DNA

ion

other

protein

RNA-only

RNA family global

RNA/DNA_hybrid

TAR_rna

aptamer_rna

mRNA

multiple

rRNA

riboswitch

ribozyme

snRNA

sre_rna

synthetic construct

tRNA

telomerase_RNA

unknown

RNA family chains

aptamer_rna

mRNA

riboswitch

ribozyme

RNA/DNA_hybrid

rRNA

snRNA

sre_rna

synthetic construct

TAR_rna

telomerase_RNA

tRNA

unknown

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