HARIBOSS

Harnessing RIBOnucleic acid - Small molecules Structures

Compounds
RNA-SM complexes
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compounds

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)

0EC

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Molecular weight: 289.15 g/mol

0G

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Molecular weight: 363.06 g/mol

13T

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Molecular weight: 594.34 g/mol

1F2

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Molecular weight: 788.46 g/mol

1F3

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Molecular weight: 842.47 g/mol

1F4

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Molecular weight: 816.49 g/mol

1FZ

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Molecular weight: 481.01 g/mol

1GC

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Molecular weight: 505.02 g/mol

1PE

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Molecular weight: 238.14 g/mol

1TU

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Molecular weight: 254.09 g/mol

218

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Molecular weight: 259.16 g/mol

29G

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Molecular weight: 162.07 g/mol

29H

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Molecular weight: 163.05 g/mol

2AD

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Molecular weight: 266.11 g/mol

2BA

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Molecular weight: 658.11 g/mol

2DA

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Molecular weight: 315.07 g/mol

2KH

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Molecular weight: 482.99 g/mol

2QB

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Molecular weight: 164.08 g/mol

2QC

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Molecular weight: 191.05 g/mol

2TB

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Molecular weight: 164.12 g/mol

2TM

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Molecular weight: 481.01 g/mol

2ZY

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Molecular weight: 320.06 g/mol

2ZZ

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Molecular weight: 278.01 g/mol

34G

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Molecular weight: 480.30 g/mol

38E

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Molecular weight: 252.07 g/mol

3AT

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Molecular weight: 491.00 g/mol

3H3

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Molecular weight: 457.25 g/mol

3HE

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Molecular weight: 281.16 g/mol

3J2

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Molecular weight: 362.14 g/mol

3J6

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Molecular weight: 296.13 g/mol

3K5

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Molecular weight: 804.32 g/mol

3K8

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Molecular weight: 377.20 g/mol

3KD

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Molecular weight: 287.12 g/mol

3KF

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Molecular weight: 307.07 g/mol

3L2

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Molecular weight: 502.22 g/mol

3LK

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Molecular weight: 578.38 g/mol

3QB

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Molecular weight: 406.21 g/mol

3TS

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Molecular weight: 739.30 g/mol

3V6

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Molecular weight: 380.09 g/mol

4BW

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Molecular weight: 674.10 g/mol

4M2

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Molecular weight: 802.34 g/mol

4PQ

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Molecular weight: 220.09 g/mol

51B

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Molecular weight: 382.16 g/mol

53D

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Molecular weight: 443.27 g/mol

5AD

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Molecular weight: 251.10 g/mol

5GP

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Molecular weight: 363.06 g/mol

5GS

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Molecular weight: 418.02 g/mol

5I0

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Molecular weight: 602.30 g/mol

62B

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Molecular weight: 507.30 g/mol

6EK

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Molecular weight: 658.22 g/mol

6GO

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Molecular weight: 165.07 g/mol

6GS

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Molecular weight: 420.01 g/mol

6GU

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Molecular weight: 169.02 g/mol

6HS

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Molecular weight: 448.25 g/mol

6IF

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Molecular weight: 494.22 g/mol

6MN

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Molecular weight: 259.05 g/mol

6YG

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Molecular weight: 383.14 g/mol

747

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Molecular weight: 281.06 g/mol

74G

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Molecular weight: 751.33 g/mol

773

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Molecular weight: 765.42 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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