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)

KSG

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Molecular weight: 379.16 g/mol

KWL

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Molecular weight: 334.19 g/mol

KWU

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Molecular weight: 173.10 g/mol

KXC

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Molecular weight: 230.15 g/mol

KY6

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Molecular weight: 359.11 g/mol

L8H

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Molecular weight: 173.08 g/mol

L94

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Molecular weight: 336.30 g/mol

LC2

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Molecular weight: 459.23 g/mol

LHA

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Molecular weight: 863.45 g/mol

LIV

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Molecular weight: 761.35 g/mol

LLL

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Molecular weight: 449.29 g/mol

LMA

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Molecular weight: 830.50 g/mol

LQQ

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Molecular weight: 447.24 g/mol

LSS

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Molecular weight: 459.15 g/mol

LUJ

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Molecular weight: 641.35 g/mol

LUM

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Molecular weight: 242.08 g/mol

LXI

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Molecular weight: 444.07 g/mol

LXR

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Molecular weight: 412.10 g/mol

LYA

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Molecular weight: 427.15 g/mol

M2D

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Molecular weight: 503.26 g/mol

M5Z

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Molecular weight: 731.36 g/mol

M7M

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Molecular weight: 487.09 g/mol

MES

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Molecular weight: 195.06 g/mol

MGR

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Molecular weight: 329.20 g/mol

MIV

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Molecular weight: 695.42 g/mol

MIX

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Molecular weight: 444.20 g/mol

MIY

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Molecular weight: 457.19 g/mol

MMP

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Molecular weight: 580.31 g/mol

MQ6

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Molecular weight: 531.25 g/mol

MQC

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Molecular weight: 306.15 g/mol

MT9

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Molecular weight: 469.30 g/mol

MTA

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Molecular weight: 297.09 g/mol

MUL

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Molecular weight: 493.32 g/mol

MVM

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Molecular weight: 433.14 g/mol

MYC

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Molecular weight: 318.04 g/mol

MYL

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Molecular weight: 503.27 g/mol

N30

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Molecular weight: 454.23 g/mol

N33

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Molecular weight: 514.25 g/mol

N5C

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Molecular weight: 527.97 g/mol

N6E

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Molecular weight: 521.01 g/mol

NAD

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Molecular weight: 663.11 g/mol

NAI

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Molecular weight: 665.13 g/mol

NAZ

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Molecular weight: 459.20 g/mol

NEG

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Molecular weight: 248.15 g/mol

NI4

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Molecular weight: 361.18 g/mol

NJL

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Molecular weight: 356.10 g/mol

NMN

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Molecular weight: 335.06 g/mol

NMY

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Molecular weight: 614.31 g/mol

NMZ

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Molecular weight: 717.36 g/mol

NNR

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Molecular weight: 255.10 g/mol

NPR

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Molecular weight: 255.10 g/mol

NWX

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Molecular weight: 531.00 g/mol

O00

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Molecular weight: 340.10 g/mol

O2I

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Molecular weight: 365.10 g/mol

O7S

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Molecular weight: 557.29 g/mol

O7V

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Molecular weight: 717.32 g/mol

O7Y

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Molecular weight: 713.31 g/mol

O8D

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Molecular weight: 553.28 g/mol

O8J

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Molecular weight: 527.26 g/mol

O8P

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Molecular weight: 741.20 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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