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)

27 Complexes found

Complexes per page

60 120 180

filters used: RNA family global: TAR_rna

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HIV-2 TAR-ARGININAMIDE COMPLEX, NMR, 20 STRUCTURES

SM: ARG

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HIV-2 TRANS ACTIVATING REGION RNA COMPLEX WITH ARGININAMIDE, NMR, MINIMIZED AVERAGE STRUCTURE

SM: ARG

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ARG-BOUND TAR RNA, NMR

SM: ARG

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STRUCTURE OF TAR RNA COMPLEXED WITH A TAT-TAR INTERACTION NANOMOLAR INHIBITOR THAT WAS IDENTIFIED BY COMPUTATIONAL SCREENING

SM: PMZ

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Designed HIV-1 TAR Binding Ligand

SM: P13

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NMR structure of a synthetic small molecule, rbt203, bound to HIV-1 TAR RNA

SM: P14

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

SM: P12

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HIV-1 subtype A genomic RNA Dimerization Initiation Site

SM: SPM

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HIV-1 DIS kissing-loop in complex with neamine

SM: XXX

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HIV-1 DIS kissing-loop in complex with Neomycin

SM: NMY

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HIV-1 DIS kissing-loop in complex with ribostamycin

SM: RIO

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HIV-1 DIS kissing-loop in complex with lividomycin

SM: LIV

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guanidino neomycin B recognition of an HIV-1 RNA helix

SM: G0B

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Chemical probe bound to HIV TAR RNA

SM: ARG L8H

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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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Crystal structure of HIV-1 subtype F DIS extended duplex RNA bound to ribostamycin

SM: RIO

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Crystal structure of HIV-1 subtype F DIS extended duplex RNA bound to paromomycin

SM: PAR

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Crystal structure of HIV-1 subtype F DIS extended duplex RNA bound to lividomycin

SM: LIV

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Crystal Structure of HIV-1 subtype F DIS extended duplex RNA bound to neomycin

SM: NMY

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Crystal structure of HIV-1 subtype F DIS extended duplex RNA bound to ribostamycin (U267OMe)

SM: RIO

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Minimal U1 snRNP

SM: EPE

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Crystal structure of HIV-1 Reverse Transcriptase in complex with RNA/DNA and dATP

SM: DTP

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Structure of HIV-1 RT complexed with RNA/DNA hybrid in the RNA hydrolysis mode

SM: TAM

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Structure of HIV-1 RT complexed with an RNA/DNA hybrid sequence non-preferred for RNA hydrolysis

SM: TAM

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

SM: LQQ

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

SM: LQQ

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

SM: LQQ

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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

Homo

Lentivirus

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]

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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