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)

O8S

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Molecular weight: 730.28 g/mol

O8V

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Molecular weight: 713.31 g/mol

OCW

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Molecular weight: 486.12 g/mol

OI9

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Molecular weight: 502.25 g/mol

OIY

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Molecular weight: 758.44 g/mol

OJI

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Molecular weight: 267.10 g/mol

ON0

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Molecular weight: 703.33 g/mol

OXG

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Molecular weight: 165.03 g/mol

OXV

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Molecular weight: 608.79 g/mol

P12

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Molecular weight: 323.23 g/mol

P13

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Molecular weight: 407.27 g/mol

P14

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Molecular weight: 353.25 g/mol

P5E

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Molecular weight: 499.95 g/mol

P8F

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Molecular weight: 551.21 g/mol

PA1

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Molecular weight: 179.08 g/mol

PAR

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Molecular weight: 615.30 g/mol

PCY

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Molecular weight: 558.27 g/mol

PEV

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Molecular weight: 719.55 g/mol

PG4

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Molecular weight: 194.12 g/mol

PGV

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Molecular weight: 748.53 g/mol

PHE

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Molecular weight: 165.08 g/mol

PMZ

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Molecular weight: 326.15 g/mol

POH

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Molecular weight: 678.32 g/mol

PP9

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Molecular weight: 562.26 g/mol

PPS

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Molecular weight: 506.99 g/mol

PQ0

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Molecular weight: 175.05 g/mol

PRF

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Molecular weight: 179.08 g/mol

PRL

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Molecular weight: 209.10 g/mol

PRP

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Molecular weight: 389.95 g/mol

PUM

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Molecular weight: 486.18 g/mol

PYI

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Molecular weight: 419.09 g/mol

PZG

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Molecular weight: 427.10 g/mol

Q1V

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Molecular weight: 714.13 g/mol

Q44

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Molecular weight: 193.06 g/mol

QAX

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Molecular weight: 317.17 g/mol

QB3

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Molecular weight: 303.16 g/mol

QEU

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Molecular weight: 346.20 g/mol

QI9

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Molecular weight: 324.18 g/mol

QIJ

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Molecular weight: 193.06 g/mol

QSA

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Molecular weight: 362.13 g/mol

QSI

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Molecular weight: 474.13 g/mol

QSV

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Molecular weight: 408.18 g/mol

QSY

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Molecular weight: 369.23 g/mol

QTZ

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Molecular weight: 727.41 g/mol

QU2

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Molecular weight: 711.42 g/mol

QW4

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Molecular weight: 347.12 g/mol

R14

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Molecular weight: 749.39 g/mol

RAP

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Molecular weight: 913.56 g/mol

RBF

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Molecular weight: 376.14 g/mol

RCG

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Molecular weight: 505.21 g/mol

RD8

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Molecular weight: 438.18 g/mol

RFP

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Molecular weight: 822.41 g/mol

RIO

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Molecular weight: 454.23 g/mol

ROS

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Molecular weight: 343.18 g/mol

ROX

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Molecular weight: 836.53 g/mol

RPO

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Molecular weight: 705.34 g/mol

RS3

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Molecular weight: 405.17 g/mol

RTP

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Molecular weight: 483.98 g/mol

RU6

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Molecular weight: 971.58 g/mol

S81

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Molecular weight: 324.18 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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