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)

S8L

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Molecular weight: 466.98 g/mol

S96

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Molecular weight: 572.98 g/mol

S9F

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Molecular weight: 524.19 g/mol

SAH

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Molecular weight: 384.12 g/mol

SAM

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Molecular weight: 398.14 g/mol

SCM

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Molecular weight: 332.16 g/mol

SFG

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Molecular weight: 381.18 g/mol

SGV

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Molecular weight: 309.11 g/mol

SIS

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Molecular weight: 447.27 g/mol

SJP

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Molecular weight: 669.37 g/mol

SLD

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Molecular weight: 513.20 g/mol

SLZ

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Molecular weight: 164.06 g/mol

SPE

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Molecular weight: 188.20 g/mol

SPK

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Molecular weight: 206.25 g/mol

SPM

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Molecular weight: 202.22 g/mol

SPS

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Molecular weight: 361.08 g/mol

SRY

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Molecular weight: 581.27 g/mol

SS0

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Molecular weight: 331.24 g/mol

SSA

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Molecular weight: 433.10 g/mol

SY5

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Molecular weight: 305.21 g/mol

T0A

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Molecular weight: 166.09 g/mol

T1C

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Molecular weight: 587.29 g/mol

T8B

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Molecular weight: 600.13 g/mol

TAC

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Molecular weight: 444.15 g/mol

TAM

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Molecular weight: 163.12 g/mol

TAO

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Molecular weight: 813.45 g/mol

TEL

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Molecular weight: 811.47 g/mol

TEP

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Molecular weight: 180.07 g/mol

TER

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Molecular weight: 202.22 g/mol

TFX

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Molecular weight: 283.13 g/mol

TG

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Molecular weight: 332.19 g/mol

THF

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Molecular weight: 473.17 g/mol

THG

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Molecular weight: 445.17 g/mol

TIX

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Molecular weight: 378.17 g/mol

TO1

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Molecular weight: 291.10 g/mol

TOA

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Molecular weight: 180.09 g/mol

TOC

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Molecular weight: 164.12 g/mol

TOY

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Molecular weight: 467.26 g/mol

TPP

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Molecular weight: 425.04 g/mol

TPS

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Molecular weight: 345.08 g/mol

TRP

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Molecular weight: 204.09 g/mol

TTP

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Molecular weight: 481.99 g/mol

U3B

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Molecular weight: 556.29 g/mol

U3H

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Molecular weight: 469.99 g/mol

U5P

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Molecular weight: 324.04 g/mol

U7V

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Molecular weight: 370.12 g/mol

U7Y

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Molecular weight: 370.12 g/mol

UAM

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Molecular weight: 423.20 g/mol

UCX

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Molecular weight: 555.27 g/mol

UDF

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Molecular weight: 867.93 g/mol

UDP

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Molecular weight: 404.00 g/mol

UE6

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Molecular weight: 698.36 g/mol

UEC

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Molecular weight: 746.36 g/mol

UG1

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Molecular weight: 203.08 g/mol

UG4

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Molecular weight: 203.08 g/mol

UH0

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Molecular weight: 570.24 g/mol

UI0

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Molecular weight: 743.33 g/mol

UI9

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Molecular weight: 445.11 g/mol

UIF

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Molecular weight: 778.29 g/mol

ULR

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Molecular weight: 382.19 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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