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)

536 compounds found

compounds per page

60 120 180

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PDB Ligand ID (ascending) PDB Ligand ID (descending) Molecular weight (ascending) Molecular weight (descending) lipinski ok (ascending) lipinski ok (descending) Veber ok (ascending) Veber ok (descending) Pfizer ok (ascending) Pfizer ok (descending)

GH3

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Molecular weight: 507.00 g/mol

GIR

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Molecular weight: 190.06 g/mol

GLP

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Molecular weight: 259.05 g/mol

GMI

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Molecular weight: 423.07 g/mol

GMP

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Molecular weight: 283.09 g/mol

GND

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Molecular weight: 175.12 g/mol

GNG

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Molecular weight: 267.10 g/mol

GNP

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Molecular weight: 522.01 g/mol

GP3

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Molecular weight: 788.07 g/mol

GSP

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Molecular weight: 538.97 g/mol

GSU

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Molecular weight: 475.11 g/mol

GTP

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Molecular weight: 522.99 g/mol

GZ4

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Molecular weight: 361.17 g/mol

GZ7

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Molecular weight: 440.23 g/mol

GZG

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Molecular weight: 461.21 g/mol

H4B

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Molecular weight: 241.12 g/mol

H8T

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Molecular weight: 523.23 g/mol

HF4

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Molecular weight: 482.99 g/mol

HGR

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Molecular weight: 511.17 g/mol

HJO

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Molecular weight: 491.30 g/mol

HJR

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Molecular weight: 550.23 g/mol

HKO

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Molecular weight: 588.26 g/mol

HLV

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Molecular weight: 227.10 g/mol

HMJ

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Molecular weight: 255.13 g/mol

HMT

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Molecular weight: 545.26 g/mol

HMV

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Molecular weight: 254.14 g/mol

HN8

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Molecular weight: 301.13 g/mol

HNG

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Molecular weight: 179.08 g/mol

HRG

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Molecular weight: 188.13 g/mol

HUV

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Molecular weight: 531.01 g/mol

HY0

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Molecular weight: 527.23 g/mol

HYG

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Molecular weight: 527.23 g/mol

HZD

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Molecular weight: 750.32 g/mol

HZG

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Molecular weight: 348.13 g/mol

IDG

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Molecular weight: 178.10 g/mol

IEL

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Molecular weight: 187.13 g/mol

IHP

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Molecular weight: 659.86 g/mol

ILA

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Molecular weight: 458.17 g/mol

ISH

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Molecular weight: 317.22 g/mol

ISI

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Molecular weight: 317.22 g/mol

J0C

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Molecular weight: 299.15 g/mol

J0D

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Molecular weight: 305.11 g/mol

J48

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Molecular weight: 500.20 g/mol

J4H

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Molecular weight: 517.23 g/mol

J8F

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Molecular weight: 303.14 g/mol

J8L

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Molecular weight: 332.18 g/mol

J8O

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Molecular weight: 305.13 g/mol

J8R

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Molecular weight: 304.13 g/mol

J8U

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Molecular weight: 330.18 g/mol

J8X

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Molecular weight: 319.13 g/mol

J93

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Molecular weight: 365.07 g/mol

JJH

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Molecular weight: 585.19 g/mol

JOS

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Molecular weight: 827.47 g/mol

JPO

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Molecular weight: 437.05 g/mol

JS4

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Molecular weight: 715.40 g/mol

JS5

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Molecular weight: 755.43 g/mol

JS6

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Molecular weight: 762.40 g/mol

K16

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Molecular weight: 466.28 g/mol

KAN

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Molecular weight: 484.24 g/mol

KKL

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Molecular weight: 304.10 g/mol

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Experimental method

Electron Microscopy

Solution NMR

X-ray

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

Acidobacterium

Acinetobacter

Alphainfluenzavirus

Alpharetrovirus

Anabaena

Arabidopsis

Archaeoglobus

Azoarcus

Bacillus

Bacteroides

Bandavirus

Betacoronavirus

Betainfluenzavirus

Bifidobacterium

Bombyx

Bos

Brassica

Caenorhabditis

Caldanaerobacter

Candida

Candidatus Korobacter

Candidatus Pelagibacter

Carnobacterium

Chlamydomonas

Clostridium

Coxiella

Cutibacterium

Cypovirus

Deinococcus

Desulfonema

Didymium

Entamoeba

Enterococcus

Enterovirus

Escherichia

Faecalibacterium

Francisella

Fusobacterium

Geobacter

Giardia

Gloeobacter

Halalkalibacterium (ex Joshi et al. 2022)

Haloarcula

Henipavirus

Hepacivirus

Homo

Ideonella

Klebsiella

Kluyveromyces

Lacticaseibacillus

Lactococcus

Leishmania

Lentivirus

Listeria

Mammarenavirus

Mesoplasma

Mesorhizobium

Mus

Mycobacterium

Mycolicibacterium

Mycoplasmoides

Neurospora

Nicotiana

Oceanobacillus

Orthobunyavirus

Orthoflavivirus

Orthonairovirus

Orthopneumovirus

Orthoreovirus

Oryctolagus

Paenibacillus

Plasmodium

Porphyromonas

Pseudomonas

Pylaiella

Pyrobaculum

Ralstonia

Rauchvirus

Roseobacter

Rotavirus

Ruminococcus

Saccharolobus

Saccharomyces

Schaalia

Segatella

Solanum

Staphylococcus

Streptococcus

Streptomyces

Sulfobacillus

Sulfolobus

Sus

Syntrophothermus

Taeniopygia

Tequatrovirus

Teseptimavirus

Tetrahymena

Thermoanaerobacter

Thermochaetoides

Thermotoga

Thermovirga

Thermus

Thogotovirus

Tilapinevirus

Tribolium

Trichoplusia

Triticum

Trypanosoma

Tymovirus

Varicellovirus

Vesiculovirus

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]

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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

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Enclosure

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Hydrophobicity

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Hydrophilicity

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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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