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)

79 Complexes found

Complexes per page

60 120 180

filters used: RNA family global: multiple

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Structure of the Arabidopsis thaliana 80S ribosome OVAC mutant in complex with P- and E-site tRNAs, mRNA, and thermospermine

SM: EPE TER

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CRYO-EM STRUCTURE OF HCT15 POLYSOMES IN HYBRID-PRE STATE

SM: HYG

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Structure of arbekacin bound Escherichia coli 70S ribosome

SM: 84G

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E. coli 70S ribosome bound to Doxycycline

SM: DXT

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E. coli 70S ribosome bound to Sarecycline

SM: V7A

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E. coli 70S ribosome bound to Minocycline

SM: MIY

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C. acnes 70S ribosome bound to Doxycycline

SM: DXT

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C. acnes 70S ribosome bound to Sarecycline

SM: V7A

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C. acnes 70S ribosome bound to Minocycline

SM: MIY

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Cryo-EM structure of SKM-70S ribosomal stalled complex in the A-tRNA positioned (Body open) state.

SM: A1JAI

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WT-HEK 80S ribosome bound to Kozak mRNA (WT-Kozak)

SM: HYG

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WT-HEK 80S ribosome bound to TISU mRNA (WT-TISU)

SM: HYG

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

SM: ANM HYG

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WT-HEK 80S ribosome bound to H2B mRNA (WT-H2B)

SM: HYG

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CRYO-EM STRUCTURE OF HUMAN 80S RIBOSOME WITH A/P/E-SITE TRNA AND MRNA CONTAINING N1-METHYLPSEUDOURIDINE

SM: HYG

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CRYO-EM STRUCTURE OF HUMAN 80S RIBOSOME WITH A/P/E-SITE TRNA AND MRNA CONTAINING URIDINE

SM: HYG

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Cryo-EM structure of SKM-70S ribosomal stalled complex in the rotated state with hybrid tRNAs

SM: A1JAI

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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

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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

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Molecular Weight

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

Current selection range: to

Deposition date

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Molecular composition of the system

RNA/Protein

Source organism

Arabidopsis

Candida

Cutibacterium

Escherichia

Giardia

Homo

Mycolicibacterium

Oryctolagus

Saccharomyces

Tequatrovirus

Thermus

Molecular weight

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Number of atoms

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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

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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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Complexes

9hes

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9i14

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9mkk

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9pih

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9pii

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9pij

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9pj7

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9pj8

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9pj9

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9qsj

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9ru7

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9ru8

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9ru9

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9ruc

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9spf

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9spi

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9sro

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9vxm

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9vxn

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