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)

11 Complexes found

Complexes per page

60 120 180

filters used: With MD simulation

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STRUCTURAL BASIS FOR RECOGNITION OF THE RNA MAJOR GROOVE IN THE TAU EXON 10 SPLICING REGULATORY ELEMENT BY AMINOGLYCOSIDE ANTIBIOTICS

SM: NMY

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2.9 A crystal structure of Streptomycin RNA-aptamer

SM: SRY

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Solution Structure of the Malachite Green RNA Binding Aptamer

SM: MGR

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NMR structure of a synthetic small molecule, rbt158, bound to HIV-1 TAR RNA

SM: P12

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Structural basis for stabilization of the tau pre-mRNA splicing regulatory element by Novantrone (Mitoxantrone)

SM: MIX

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Structure of the HIV-1 frameshift site RNA bound to a small molecule inhibitor of viral replication

SM: L94

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Structural Insight of Flavonoids binding to CAG repeat RNA that causes Huntington's Disease (HD) and Spinocerebellar Ataxia (SCAs)

SM: MYC

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Solution structure of the RNA duplex formed by the 5'-end of U1snRNA and the 5'-splice site of SMN2 exon7 in complex with the SMN-C5 splicing modifier

SM: GDZ

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Solution Structure of the Tau pre-mRNA Exon 10 Splicing Regulatory Element Bound to MQC

SM: MQC

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IRES-targeting Small Molecule Inhibits Enterovirus 71 Replication via Allosteric Stabilization of a Ternary Complex

SM: UYS

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Interaction between a fluoroquinolone derivative and RNAs with a single bulge

SM: 53D

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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

Source organism

Enterovirus

Homo

Lentivirus

Mus

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

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

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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]

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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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Complexes

1ei2

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1nta

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1q8n

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1uui

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2kgp

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2l94

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5xi1

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6hmo

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6va3

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6xb7

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7fhi

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