HARIBOSS

Harnessing RIBOnucleic acid - Small molecules Structures

Compounds
RNA-SM complexes
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compounds

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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)

DI0

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Molecular weight: 834.55 g/mol

DKM

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Molecular weight: 432.13 g/mol

DM1

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Molecular weight: 527.18 g/mol

DMY

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Molecular weight: 481.22 g/mol

DOL

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Molecular weight: 690.33 g/mol

DSH

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Molecular weight: 340.13 g/mol

DST

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Molecular weight: 261.98 g/mol

DTP

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Molecular weight: 491.00 g/mol

DUT

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Molecular weight: 467.97 g/mol

DV4

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Molecular weight: 468.22 g/mol

DX4

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Molecular weight: 167.03 g/mol

DXT

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Molecular weight: 444.15 g/mol

DZ4

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Molecular weight: 490.02 g/mol

E7X

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Molecular weight: 411.19 g/mol

EDE

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Molecular weight: 781.45 g/mol

EDS

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Molecular weight: 592.34 g/mol

EEM

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Molecular weight: 447.09 g/mol

EKJ

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Molecular weight: 407.17 g/mol

EKM

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Molecular weight: 332.13 g/mol

EM1

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Molecular weight: 844.48 g/mol

EPE

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Molecular weight: 238.10 g/mol

EQ1

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Molecular weight: 774.15 g/mol

EQ4

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Molecular weight: 428.10 g/mol

ERN

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Molecular weight: 734.49 g/mol

ERY

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Molecular weight: 733.46 g/mol

EUS

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Molecular weight: 525.25 g/mol

EZG

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Molecular weight: 349.14 g/mol

EZM

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Molecular weight: 340.18 g/mol

EZP

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Molecular weight: 349.14 g/mol

F2A

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Molecular weight: 489.02 g/mol

FAD

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Molecular weight: 785.16 g/mol

FFO

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Molecular weight: 473.17 g/mol

FH8

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Molecular weight: 431.16 g/mol

FME

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Molecular weight: 177.05 g/mol

FMN

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Molecular weight: 456.11 g/mol

FSD

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Molecular weight: 618.30 g/mol

FSJ

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Molecular weight: 450.25 g/mol

FUA

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Molecular weight: 516.35 g/mol

FXQ

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Molecular weight: 172.14 g/mol

FXT

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Molecular weight: 186.16 g/mol

G0B

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Molecular weight: 872.49 g/mol

G19

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Molecular weight: 498.25 g/mol

G2P

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Molecular weight: 521.01 g/mol

G34

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Molecular weight: 517.32 g/mol

G3A

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Molecular weight: 772.08 g/mol

G4A

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Molecular weight: 403.08 g/mol

G4P

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Molecular weight: 602.96 g/mol

G5B

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Molecular weight: 401.15 g/mol

G6M

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Molecular weight: 371.11 g/mol

G6P

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Molecular weight: 260.03 g/mol

G6V

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Molecular weight: 405.07 g/mol

G80

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Molecular weight: 477.29 g/mol

GAP

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Molecular weight: 404.09 g/mol

GCP

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Molecular weight: 521.01 g/mol

GDE

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Molecular weight: 170.02 g/mol

GDP

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Molecular weight: 443.02 g/mol

GDZ

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Molecular weight: 392.18 g/mol

GE3

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Molecular weight: 177.10 g/mol

GE6

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Molecular weight: 528.97 g/mol

GET

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Molecular weight: 496.27 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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