HARIBOSS

Harnessing RIBOnucleic acid - Small molecules Structures

Compounds
RNA-SM complexes
About

You are here

compounds

compounds

× Close

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

Sort by

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)

URI

Select this compound

Molecular weight: 244.07 g/mol

UTP

Select this compound

Molecular weight: 483.97 g/mol

UYS

Select this compound

Molecular weight: 323.15 g/mol

V5A

Select this compound

Molecular weight: 350.03 g/mol

V5Z

Select this compound

Molecular weight: 425.18 g/mol

V6D

Select this compound

Molecular weight: 541.30 g/mol

V6T

Select this compound

Molecular weight: 396.19 g/mol

V71

Select this compound

Molecular weight: 324.18 g/mol

V7A

Select this compound

Molecular weight: 487.20 g/mol

V8A

Select this compound

Molecular weight: 804.45 g/mol

V8C

Select this compound

Molecular weight: 429.17 g/mol

VDU

Select this compound

Molecular weight: 367.22 g/mol

VIB

Select this compound

Molecular weight: 265.11 g/mol

VIF

Select this compound

Molecular weight: 531.27 g/mol

VIR

Select this compound

Molecular weight: 525.25 g/mol

VK0

Select this compound

Molecular weight: 411.15 g/mol

VKI

Select this compound

Molecular weight: 855.36 g/mol

VLR

Select this compound

Molecular weight: 855.36 g/mol

VSN

Select this compound

Molecular weight: 459.00 g/mol

VTE

Select this compound

Molecular weight: 410.15 g/mol

VTR

Select this compound

Molecular weight: 565.97 g/mol

W0F

Select this compound

Molecular weight: 537.01 g/mol

W53

Select this compound

Molecular weight: 430.22 g/mol

W5Y

Select this compound

Molecular weight: 493.14 g/mol

W6F

Select this compound

Molecular weight: 763.33 g/mol

WC9

Select this compound

Molecular weight: 498.28 g/mol

WCP

Select this compound

Molecular weight: 507.19 g/mol

WIN

Select this compound

Molecular weight: 548.23 g/mol

WSB

Select this compound

Molecular weight: 481.99 g/mol

WUX

Select this compound

Molecular weight: 546.39 g/mol

WZW

Select this compound

Molecular weight: 758.51 g/mol

X0F

Select this compound

Molecular weight: 522.99 g/mol

X0O

Select this compound

Molecular weight: 497.00 g/mol

X1K

Select this compound

Molecular weight: 349.23 g/mol

X5R

Select this compound

Molecular weight: 322.08 g/mol

XBI

Select this compound

Molecular weight: 363.24 g/mol

XG4

Select this compound

Molecular weight: 506.01 g/mol

XXX

Select this compound

Molecular weight: 322.19 g/mol

Y53

Select this compound

Molecular weight: 393.22 g/mol

Y59

Select this compound

Molecular weight: 402.47 g/mol

Y7K

Select this compound

Molecular weight: 475.29 g/mol

YAT

Select this compound

Molecular weight: 480.30 g/mol

YB3

Select this compound

Molecular weight: 376.18 g/mol

YMZ

Select this compound

Molecular weight: 378.12 g/mol

YO3

Select this compound

Molecular weight: 315.15 g/mol

YQM

Select this compound

Molecular weight: 558.21 g/mol

YXM

Select this compound

Molecular weight: 558.23 g/mol

Z2V

Select this compound

Molecular weight: 400.20 g/mol

ZAN

Select this compound

Molecular weight: 506.01 g/mol

ZBA

Select this compound

Molecular weight: 464.21 g/mol

ZC0

Select this compound

Molecular weight: 408.11 g/mol

ZIT

Select this compound

Molecular weight: 748.51 g/mol

ZKP

Select this compound

Molecular weight: 310.72 g/mol

ZLD

Select this compound

Molecular weight: 337.14 g/mol

ZVM

Select this compound

Molecular weight: 359.16 g/mol

ZWB

Select this compound

Molecular weight: 427.14 g/mol

Previous
9 of 9
Go to page

Experimental method

Electron Microscopy

Solution NMR

X-ray

Experimental resolution

Select cutoff values for experimental resolution (Å)

Current selection range: to

Molecular Weight

Select cutoff values for molecular weight of the compound (Da)

Current selection range: to

Deposition date

Select cutoff values for the deposition date (years) of the PDB entries

Current selection range: to

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

Select cutoff values for molecular weight of the system complex (kDa)

Current selection range: to

Number of atoms

Select cutoff values for the number of atoms of the compounds

Current selection range: to

Number of PDB entries

Select cutoff values for the number of PDB entries where the compounds have been resolved

Current selection range: to

Number of interacting chains

Select cutoff values for the number of interacting RNA chains in the pockets

Current selection range: to

Pocket size

Select cutoff values for the number of heavy RNA atoms in the pocket

Current selection range: to

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]

Current selection range: to

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]

Current selection range: to

Exposure

Select cutoff values for the exposure, a score calculated by Schrödinger tool which indicates the degree of exposure to the solvent of the pocket (AU)

Current selection range: to

Enclosure

Select cutoff values for the enclosure, a score calculated by Schrödinger tool which indicates the degree of buriedness of the pocket (AU)

Current selection range: to

Hydrophobicity

Select cutoff values for the hydrophobicity, a score calculated by Schrödinger tool which indicates the degree of hydrophobicity of the pocket (AU)

Current selection range: to

Hydrophilicity

Select cutoff values for the hydrophilicity, a score calculated by Schrödinger tool which indicates the degree of hydrophilicity of the pocket (AU)

Current selection range: to

Donor/Acceptor

Select cutoff values for Donor/Acceptor character of the pocket calculated by Schrödinger tool

Current selection range: to

Volume

Select cutoff values for volume of the pocket calculated by Schrödinger tool (Å³)

Current selection range: to

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

25-28 Rue du Dr ROUX,
75015 Paris

About
Contact
Credits
Policies

Loading...