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)

249 Complexes found

Complexes per page

60 120 180

filters used: RNA family global: unknown

9ukt

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CryoEM structure of the T.thermophilus transcription initiation complex bound to Gp4A-C-U and CTP, -1 dC in the template DNA strand

SM: CTP

9vma

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Cryo-EM structure of substrate-bound DRT9 hexamer complex

SM: DTP

9xe6

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Crimean-Congo hemorrhagic fever virus RNA polymerase containing a 10-bp RNA product and incorporated 2FC

SM: 2KH

9xe7

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Crimean-Congo hemorrhagic fever virus RNA polymerase containing a 10-bp RNA product and incorporated cytidine

SM: 2KH

9xe9

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Crimean-Congo hemorrhagic fever virus RNA polymerase containing a 15-bp RNA product

SM: 2KH

9xec

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Crimean-Congo hemorrhagic fever virus RNA polymerase containing a 9-bp RNA product

SM: 2KH

9ymu

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De novo initial transcribing RNA polymerase with 2-mer RNA and bound CTP / Michaelis complex (RPitc2+CTP)

SM: CTP

9ynp

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Cryo-EM structure of Escherichia coli transcription initiation complex with GpA and pseudouridimycin (PUM)

SM: PUM

9ynq

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Cryo-EM structure of Escherichia coli transcription initiation complex with GpA and des-hydroxy pseudouridimycin (des-hydroxy PUM)

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Experimental method

Experimental resolution

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Molecular Weight

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Deposition date

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Molecular composition of the system

RNA

RNA/DNA

RNA/DNA/Protein

RNA/Protein

Source organism

Alphainfluenzavirus

Alpharetrovirus

Bacillus

Bacteroides

Bandavirus

Betacoronavirus

Bombyx

Caenorhabditis

Cypovirus

Desulfonema

Escherichia

Halalkalibacterium (ex Joshi et al. 2022)

Henipavirus

Homo

Klebsiella

Listeria

Mammarenavirus

Mus

Mycobacterium

Neurospora

Orthobunyavirus

Orthoflavivirus

Orthonairovirus

Orthopneumovirus

Orthoreovirus

Rauchvirus

Rotavirus

Saccharolobus

Saccharomyces

Segatella

Streptococcus

Streptomyces

Taeniopygia

Thermus

Thogotovirus

Tilapinevirus

Trichoplusia

Trypanosoma

Varicellovirus

Vesiculovirus

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

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Pocket size

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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]

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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)

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Enclosure

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Hydrophobicity

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

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Hydrophilicity

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

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Donor/Acceptor

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Volume

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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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