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)

A1LVZ

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Molecular weight: 632.90 g/mol

A1LXN

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Molecular weight: 165.07 g/mol

A1LYK

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Molecular weight: 283.12 g/mol

A1LYL

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Molecular weight: 269.15 g/mol

A1ME1

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Molecular weight: 554.98 g/mol

A5A

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Molecular weight: 417.11 g/mol

AB6

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Molecular weight: 524.32 g/mol

AB9

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Molecular weight: 509.32 g/mol

ADN

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Molecular weight: 267.10 g/mol

ADP

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Molecular weight: 427.03 g/mol

AKN

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Molecular weight: 585.29 g/mol

AM2

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Molecular weight: 539.28 g/mol

AMO

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Molecular weight: 462.09 g/mol

AMP

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Molecular weight: 347.06 g/mol

AMR

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Molecular weight: 229.05 g/mol

AMZ

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Molecular weight: 338.06 g/mol

ANG

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Molecular weight: 166.06 g/mol

ANM

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Molecular weight: 265.13 g/mol

APC

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Molecular weight: 505.02 g/mol

AQJ

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Molecular weight: 525.33 g/mol

ARG

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Molecular weight: 175.12 g/mol

AT9

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Molecular weight: 539.00 g/mol

ATP

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Molecular weight: 507.00 g/mol

B2R

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Molecular weight: 503.23 g/mol

B3P

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Molecular weight: 282.18 g/mol

B6M

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Molecular weight: 615.30 g/mol

BDG

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Molecular weight: 178.10 g/mol

BER

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Molecular weight: 336.12 g/mol

BFT

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Molecular weight: 468.12 g/mol

BLS

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Molecular weight: 422.20 g/mol

BTB

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Molecular weight: 209.13 g/mol

BTN

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Molecular weight: 244.09 g/mol

C2E

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Molecular weight: 690.10 g/mol

C5P

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Molecular weight: 323.05 g/mol

CBV

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Molecular weight: 400.96 g/mol

CDP

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Molecular weight: 403.02 g/mol

CH1

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Molecular weight: 466.99 g/mol

CIR

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Molecular weight: 175.10 g/mol

CIT

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Molecular weight: 192.03 g/mol

CLM

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Molecular weight: 322.01 g/mol

CLY

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Molecular weight: 424.18 g/mol

CMG

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Molecular weight: 247.14 g/mol

CNY

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Molecular weight: 596.30 g/mol

CPF

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Molecular weight: 331.13 g/mol

CSG

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Molecular weight: 482.00 g/mol

CTC

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Molecular weight: 478.11 g/mol

CTI

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Molecular weight: 348.12 g/mol

CTP

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Molecular weight: 482.99 g/mol

CTY

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Molecular weight: 747.48 g/mol

CYY

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Molecular weight: 162.10 g/mol

D2C

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Molecular weight: 452.14 g/mol

D2X

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Molecular weight: 426.03 g/mol

D3T

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Molecular weight: 465.99 g/mol

D4M

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Molecular weight: 304.05 g/mol

DAI

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Molecular weight: 375.18 g/mol

DCP

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Molecular weight: 466.99 g/mol

DCT

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Molecular weight: 451.00 g/mol

DGP

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Molecular weight: 347.06 g/mol

DGT

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Molecular weight: 507.00 g/mol

DHF

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Molecular weight: 443.16 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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