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)

616 Complexes found

Complexes per page

60 120 180

filters used: Molecule type: RNA

9ol3

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DNA-imidazolium-bridged dinucleotide intermediate complex

9pde

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Three-dimensional structure of kinase inhibitor Palbociclib-HIV TAR complex

SM: LQQ

9pdf

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Three-dimensional structure of kinase inhibitor Palbociclib-HIV TAR complex

SM: LQQ

9pdg

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Three-dimensional structure of kinase inhibitor Palbociclib-HIV TAR complex

SM: LQQ

9q0i

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Structure of dsRNA 16mer containing 4'-C-methyladenosine

SM: SPM

9uw0

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Crystal structure of 2'-dG-III riboswitch with Guanosine, manganese saok

SM: GMP

9v4u

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Crystal structure of Guanine-II riboswitch in complex with 7,8-dihydroneopterin

SM: NPR

9v4v

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Crystal structure of Guanine-II riboswitch in complex with isoxanthopterin

SM: 7PD

9v4y

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Crystal structure of Guanine-II riboswitch in complex with 8-aminoguanine

SM: ANG

9v4z

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Crystal structure of Guanine-II riboswitch in complex with 8-oxoguanine

SM: OXG

9v50

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Crystal structure of Guanine-II riboswitch in complex with 8-methylguanine

9v51

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Crystal structure of Guanine-II riboswitch in complex with tetrahydrobiopterin

SM: H4B

9v7n

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Cryo-EM structures of the Azoarcus pre-tRNA(ILE) conformation a undergoing the first-step self-splicing

SM: GMP

9v7o

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Cryo-EM structures of the Azoarcus pre-tRNA(ILE) conformation b undergoing the first-step self-splicing

SM: GMP

9vmz

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Crystal structure of Broccoli aptamer in with BI

9yd3

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RNA primer non-enzymatic extension product with RNA substrate

SM: EQ4

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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

Alpharetrovirus

Anabaena

Arabidopsis

Azoarcus

Bacillus

Caldanaerobacter

Candida

Candidatus Korobacter

Candidatus Pelagibacter

Carnobacterium

Clostridium

Deinococcus

Didymium

Enterovirus

Escherichia

Faecalibacterium

Fusobacterium

Geobacter

Gloeobacter

Hepacivirus

Homo

Ideonella

Lacticaseibacillus

Lactococcus

Leishmania

Lentivirus

Mesoplasma

Mesorhizobium

Mus

Mycobacterium

Oceanobacillus

Paenibacillus

Pseudomonas

Pylaiella

Ralstonia

Roseobacter

Saccharomyces

Schaalia

Staphylococcus

Streptococcus

Streptomyces

Sulfobacillus

Syntrophothermus

Tetrahymena

Thermoanaerobacter

Thermotoga

Thermovirga

Tymovirus

Varicellovirus

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

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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

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

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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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