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)

87 Complexes found

Complexes per page

60 120 180

filters used: With binding affinity values

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Crystal structure of Bacillus subtilis cyclic-di-AMP riboswitch ydaO

SM: 2BA

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Crystal structure of the ZMP riboswitch at 1.80 angstrom

SM: AMZ

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3',3'-cGAMP riboswitch bound with 3',3'-cGAMP

SM: 4BW

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3',3'-cGAMP riboswitch bound with c-di-GMP

SM: C2E

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The structure of A pfI Riboswitch Bound to ZMP

SM: AMZ

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Fusobacterium ulcerans ZTP riboswitch bound to ZMP

SM: AMZ

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Structure of a 5-hydroxytryptophan aptamer

SM: 4PQ

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Solution NMR structure of the GTP binding Class II RNA aptamer-ligand-complex containing a protonated adenine nucleotide with a highly shifted pKa.

SM: GTP

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RNA primer-template complex with guanosine dinucleotide ligand G(5')ppp(5')G

SM: GP3

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Co-crystal structure of the fluorogenic RNA Mango

SM: 74G

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Crystal Structure of the Mango-II Fluorescent Aptamer Bound to TO1-Biotin

SM: EKJ

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Crystal Structure of the Mango-II Fluorescent Aptamer Bound to TO3-Biotin

SM: EKM

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Crystal Structure of the Mango-II-A22U Fluorescent Aptamer Bound to TO1-Biotin

SM: EKJ

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G96A mutant of the PRPP riboswitch from T. mathranii bound to ppGpp

SM: G4P GTP

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PRPP riboswitch from T. mathranii bound to PRPP

SM: PRP

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PRPP Riboswitch bound to PRPP, native structure

SM: PRP

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ppGpp Riboswitch bound to ppGpp, native structure

SM: G4P

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Crystal structure of the Corn aptamer in complex with ThT

SM: TFX

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Crystal structure of the Corn aptamer in complex with TO

SM: J0D

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Structure of the iMango-III aptamer bound to TO1-Biotin

SM: EKJ SPM

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Structure of the Mango-III (A10U) aptamer bound to TO1-Biotin

SM: HZG

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Structure of the Mango-III (A10U) aptamer bound to TO1-Biotin

SM: HZD

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Crystal structure of the metY SAM V riboswitch

SM: SAM

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The structure of the SAM/SAH-binding riboswitch.

SM: SAH

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The structure of the G. violaceus guanidine II riboswitch P2 stem-loop with arcaine

SM: FXQ

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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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Structural basis for 2'-deoxyguanosine recognition by the 2'-dG-II class of riboswitches

SM: GNG

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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/Protein

Source organism

Bacillus

Caldanaerobacter

Candidatus Pelagibacter

Clostridium

Escherichia

Faecalibacterium

Geobacter

Gloeobacter

Hepacivirus

Homo

Lacticaseibacillus

Lentivirus

Mesoplasma

Ralstonia

Schaalia

Streptococcus

Streptomyces

Sulfobacillus

Syntrophothermus

Thermoanaerobacter

Thermovirga

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

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]

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)

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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

Select cutoff values for volume of the pocket calculated by Schrödinger tool (Å³)

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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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