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)

267 Complexes found

Complexes per page

60 120 180

filters used: RNA family global: riboswitch

8xzn

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Crystal structure of folE riboswitch with BH4

8xzo

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Crystal structure of folE riboswitch with Guanine

SM: SPM

8xzp

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Crystal structure of folE riboswitch with 8-CH3 Guanine

8xzq

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Crystal structure of folE riboswitch with 8-N Guanine

SM: SPM

8xzr

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Crystal structure of folE riboswitch with 8-NH2 Guanine

8xzw

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Crystal structure of THF-II riboswitch with THF and soaked with Ir

8yam

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Crystal structure of a class I PreQ1 riboswitch complexed with a synthetic compound

8yan

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Crystal structure of a class I PreQ1 riboswitch complexed with a synthetic compound

9bzc

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Cocrystal structure of Clostridium beijerinckii ZTP riboswitch with ZMP and Cs

SM: AMZ

9c6k

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Cryo-EM structure of the TPP riboswitch embedded in an RNA scaffold bound to thiamine pyrophosphate

SM: TPP

9ebp

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Structure of the Bacillus subtilis yjdF riboswitch complexed with lumichrome in the presence of iridium hexammine

SM: LUM

9ebv

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Structure of the Bacillus subtilis yjdF riboswitch aptamer domain in complex with lumichrome

SM: LUM

9ec4

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Structure of the Bacillus subtilis yjdF riboswitch aptamer domain in complex with chelerythrine

SM: CTI

9hro

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Solution NMR structure of the synthetic tobramycin riboswitch in complex with tobramycin

SM: TOY

9lkc

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Crystal structure of Guanine-II riboswitch in complex with 2'-deoxyguanosine

SM: GNG

9lkf

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Crystal structure of Guanine-II riboswitch in complex with guanosine

SM: GMP

9lku

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Crystal structure of the 2'-dG-III riboswitch bound to Guanosine

SM: GMP

9lkv

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Crystal structure of the 2'-dG-III riboswitch bound to 2'-dG

SM: GNG

9nbc

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RNA scaffold attached to 8-oxoguanine riboswitch aptamer

SM: OXG

9ndd

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RNA scaffold attached to 8-oxoguanine riboswitch aptamer, combined core plus aptamer

SM: OXG

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

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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

Acidobacterium

Arabidopsis

Bacillus

Bifidobacterium

Caldanaerobacter

Candidatus Korobacter

Candidatus Pelagibacter

Carnobacterium

Clostridium

Escherichia

Faecalibacterium

Fusobacterium

Geobacter

Gloeobacter

Hepacivirus

Homo

Ideonella

Lacticaseibacillus

Lactococcus

Mesoplasma

Mesorhizobium

Mycobacterium

Paenibacillus

Pseudomonas

Ralstonia

Roseobacter

Ruminococcus

Schaalia

Staphylococcus

Streptococcus

Sulfobacillus

Syntrophothermus

Thermoanaerobacter

Thermotoga

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

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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

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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