HARIBOSS

Harnessing RIBOnucleic acid - Small molecules Structures

Compounds
RNA-SM 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)

265 Complexes found

Complexes per page

60 120 180

filters used: RNA environment global: RNA/Other

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In situ human A-P-E state 80S ribosome

SM: SPM

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In situ human eEF1A-A/T-P-E state 80S ribosome

SM: SPM

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In situ human Hibernating class1 (rotate3) without E tRNA state 80S ribosome

SM: SPM

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In situ human A/P-P/E state 80S ribosome

SM: SPM

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In situ HHT and CHX treated human P-Z state 80S ribosome

SM: 3HE HMT SPM

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In situ human unrotated hibernating with CCDC124 state 80S ribosome

SM: SPM

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In situ human unrotated hibernating without CCDC124 state 80S ribosome

SM: SPM

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In situ human 60S ribosome

SM: SPM

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In situ human 60S ribosome with EIF6

SM: SPM

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In situ human 80S consensus ribosome with EBP1

SM: SPM

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In situ human 80S ribosome (composite map)

SM: SPM

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In situ structure of the human mitoribosome in the P-E state

SM: NAD SPM

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In situ structure of the human mitoribosome in the P state

SM: NAD SPM

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E. coli 70S ribosome bound to Doxycycline

SM: DXT

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C. acnes 70S ribosome bound to Doxycycline

SM: DXT

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In situ HHT and CHX treated human hibernating state 80S ribosome

SM: 3HE HMT SPM

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In situ CHX and HHT treated 80S consensus ribosome

SM: 3HE HMT SPM

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In situ human P state 80S ribosome

SM: SPM

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

SM: ANM HYG

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Structure at 1.9 A resolution of Thermus thermophilus tyrosyl-tRNA synthetase bound to wild-type tRNATyr(GUC).

SM: 1PE

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

SM: FUA GDP

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

SM: FUA GDP

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

SM: DXT

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70S Coxiella burnetii Ribosome with Doxycycline and HPFcold

SM: DXT

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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

Select cutoff values for molecular weight of the system complex (kDa)

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

RNA/DNA/Protein

RNA/Protein

Source organism

Acinetobacter

Alphainfluenzavirus

Arabidopsis

Bacteroides

Betacoronavirus

Caenorhabditis

Caldanaerobacter

Candida

Carnobacterium

Coxiella

Cutibacterium

Deinococcus

Desulfonema

Escherichia

Haloarcula

Homo

Leishmania

Mesorhizobium

Neurospora

Pseudomonas

Pyrobaculum

Roseobacter

Saccharolobus

Saccharomyces

Staphylococcus

Thermotoga

Thermus

Varicellovirus

Molecular weight

Select cutoff values for molecular weight of the compound (Da)

Current selection range: to

Number of atoms

Select cutoff values for the number of atoms of the compounds

Current selection range: to

Number of PDB entries

Select cutoff values for the number of PDB entries where the compounds have been resolved

Current selection range: to

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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