HARIBOSS

Harnessing RIBOnucleic acid - Small molecules Structures

Compounds
RNA-SM complexes
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Complexes

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)

1894 Complexes found

Complexes per page

60 120 180

filters used: With equivalence class

4khp

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Structure of the Thermus thermophilus 30S ribosomal subunit in complex with de-6-MSA-pactamycin

4kqy

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Bacillus subtilis yitJ S box/SAM-I riboswitch

SM: SAM

4kzd

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Crystal structure of an RNA aptamer in complex with fluorophore and Fab

SM: 1TU

4l47

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Crystal Structure of Frameshift Suppressor tRNA SufA6 Bound to Codon CCC-U on the Ribosome

SM: PAR

4l71

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Crystal Structure of Frameshift Suppressor tRNA SufA6 Bound to Codon CCC-A on the Ribosome

SM: PAR

4l81

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Structure of the SAM-I/IV riboswitch (env87(deltaU92, deltaG93))

SM: SAM

4lel

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Crystal Structure of Frameshift Suppressor tRNA SufA6 Bound to Codon CCG-G on the Ribosome

SM: PAR

4lf4

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Crystal Structure of 30S ribosomal subunit from Thermus thermophilus

SM: LLL

4lf5

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Crystal Structure of 30S ribosomal subunit from Thermus thermophilus

SM: HYG

4lf6

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Crystal Structure of 30S ribosomal subunit from Thermus thermophilus

SM: NMY

4lf7

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Crystal Structure of 30S ribosomal subunit from Thermus thermophilus

SM: PAR

4lf8

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Crystal Structure of 30S ribosomal subunit from Thermus thermophilus

SM: PAR

4lf9

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Crystal Structure of 30S ribosomal subunit from Thermus thermophilus

SM: LLL

4lfa

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Crystal Structure of 30S ribosomal subunit from Thermus thermophilus

SM: HYG

4lfb

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Crystal Structure of 30S ribosomal subunit from Thermus thermophilus

SM: NMY

4lfc

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Crystal Structure of 30S ribosomal subunit from Thermus thermophilus

SM: TOY

4lfz

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Crystal Structure of Frameshift Suppressor tRNA SufA6 Bound to Codon CCC-U in the Absence of Paromomycin

SM: AMP

4lnt

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Crystal Structure of tRNA Proline (CGG) Bound to Codon CCC-U on the Ribosome

SM: PAR

4lsk

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Crystal Structure of tRNA Proline (CGG) Bound to Codon CCG-G on the Ribosome

SM: PAR

4lt8

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Crystal Structure of tRNA Proline (CGG) Bound to Codon CCC-G on the Ribosome

SM: PAR

4lvv

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Structure of the THF riboswitch

SM: FFO

4lvx

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Structure of the THF riboswitch bound to tetrahydrobiopterin

SM: H4B

4lvy

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Structure of the THF riboswitch bound to pemetrexed

SM: LYA

4lx5

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X-ray crystal structure of the M6" riboswitch aptamer bound to pyrimido[4,5-d]pyrimidine-2,4-diamine (PPDA)

SM: 29G

4lx6

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X-ray crystal structure of the M6C" riboswitch aptamer bound to 2-aminopyrimido[4,5-d]pyrimidin-4(3H)-one (PPAO)

SM: 29H

4m2z

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Crystal structure of RNASE III complexed with double-stranded RNA and CMP (TYPE II CLEAVAGE)

SM: C5P

4m30

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Crystal structure of RNASE III complexed with double-stranded RNA AND AMP (TYPE II CLEAVAGE)

SM: AMP

4n48

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Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1 Protein in complex with capped RNA fragment

SM: SAM

4nfo

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Crystal Structure Analysis of the 16mer GCAGACUUAAGUCUGC

SM: SPM

4nxn

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Crystal Structure of the 30S ribosomal subunit from a GidB (RsmG) mutant of Thermus thermophilus (HB8), bound with streptomycin

SM: SRY

4nya

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Crystal structure of the E. coli thiM riboswitch in complex with 5-(azidomethyl)-2-methylpyrimidin-4-amine

SM: 2QB

4nyb

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Crystal structure of the E. coli thiM riboswitch in complex with (4-(1,2,3-thiadiazol-4-yl)phenyl)methanamine

SM: 2QC

4nyg

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Crystal structure of the E. coli thiM riboswitch in complex with thiamine

SM: VIB

4o8j

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Crystal structure of RtcA, the RNA 3'-terminal phosphate cyclase from Pyrococcus horikoshii, in complex with rACAAA3'phosphate and adenine.

SM: ADN

4oqu

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Structure of the SAM-I/IV riboswitch (env87(deltaU92))

SM: SAM

4ox9

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Crystal structure of the aminoglycoside resistance methyltransferase NpmA bound to the 30S ribosomal subunit

SM: SFG

4p20

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Crystal structures of the bacterial ribosomal decoding site complexed with amikacin

SM: AKN

4p3s

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Crystal structure of the bacterial A1408C-mutant ribosomal decoding site in complex with geneticin

SM: GET

4p5j

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Crystal structure of the tRNA-like structure from Turnip Yellow Mosaic Virus (TYMV), a tRNA mimicking RNA

SM: SPM

4p6f

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Crystal structure of the peptolide 12C bound to bacterial ribosome

SM: PAR

4p70

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Crystal Structure of Unmodified tRNA Proline (CGG) Bound to Codon CCG on the Ribosome

SM: PAR

4pdq

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Crystal structure of the bacterial ribosomal decoding site in complex with 4'-deoxy-4'-fluoro neomycin analog

SM: NMZ

4pjo

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Minimal U1 snRNP

SM: EPE

4pqu

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Crystal structure of HIV-1 Reverse Transcriptase in complex with RNA/DNA and dATP

SM: DTP

4q9q

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Crystal structure of an RNA aptamer bound to bromo-ligand analog in complex with Fab

SM: 2ZZ

4q9r

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Crystal structure of an RNA aptamer bound to trifluoroethyl-ligand analog in complex with Fab

SM: 2ZY

4qk8

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Thermoanaerobacter pseudethanolicus c-di-AMP riboswitch

SM: 2BA

4qk9

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Thermovirga lienii c-di-AMP riboswitch

SM: 2BA

4qka

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c-di-AMP riboswitch from Thermoanaerobacter pseudethanolicus, iridium hexamine soak

SM: 2BA

4qlm

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ydao riboswitch binding to c-di-AMP

SM: 2BA

4qln

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structure of ydao riboswitch binding with c-di-dAMP

SM: 2BA

4qvi

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Crystal structure of mutant ribosomal protein M218L TthL1 in complex with 80nt 23S RNA from Thermus thermophilus

SM: MES

4r0d

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Crystal structure of a eukaryotic group II intron lariat

SM: SPM

4rdx

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Structure of histidinyl-tRNA synthetase in complex with tRNA(His)

SM: AMP

4rzd

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Crystal Structure of a PreQ1 Riboswitch

SM: PRF

4ts0

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Crystal structure of the Spinach RNA aptamer in complex with DFHBI, barium ions

SM: 38E

4ts2

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Crystal structure of the Spinach RNA aptamer in complex with DFHBI, magnesium ions

SM: 38E

4tua

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Crystal structure of ASL-Thr bound to Codon ACC-A on the Ribosome

SM: PAR

4tub

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Crystal structure of tRNA-Thr bound to Codon ACC-C on the Ribosome

SM: PAR

4tud

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Crystal structure of ASL-SufJ bound to Codon ACC-C on the Ribosome

SM: PAR

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Experimental method

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

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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