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

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 Non-redundant only

1000 Complexes found

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Structures of small molecules bound to RNA repeat expansions that cause Huntington's disease-like 2 and myotonic dystrophy type 1

SM:

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Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with lasso peptide lariocidin and protein Y at 2.60A resolution

SM: ARG

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Rous sarcoma virus frameshifting pseudoknot RNA

SM: TAM

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NMR structures of small molecules bound to a model of an RNA CAG repeat expansion.

SM:

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RhoBAST RNA aptamer in complex with the SpyRho555 analogue, MaP555

SM:

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Cryo-EM structure of the Pyrobaculum calidifontis 50S ribosomal subunit in complex with Dri

SM: SPM

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Cryo-EM structure of the Pyrobaculum calidifontis 70S ribosome

SM: SPM

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Cryo-EM structure of the Pyrobaculum calidifontis 70S ribosome in complex with Dri

SM: SPM

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Mammalian ternary complex of a translating 80S ribosome, NAC and NatA/E

SM: SPM

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Mammalian quaternary complex of a translating 80S ribosome, NAC, MetAP1 and NatA/E

SM: SPM

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Mammalian quaternary complex of a translating 80S ribosome, NAC, MetAP1 and NatA/E-HYPK

SM: SPM

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Structure of E. coli 30S-IF1-IF3-mRNA-Kasugamycin complex

SM: KSG

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Structure of E. coli 30S-IF1-IF3-mRNA-Edeine complex

SM: EDE

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High-resolution cryo-EM structure of Saccharolobus solfataricus 30S ribosomal subunit bound to mRNA and initiator tRNA

SM: SPM

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Crystal structure of the alkyltransferase ribozyme SAMURI co-crystallized with SAM

SM: SAH

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Crystal structure of the alkyltransferase ribozyme SAMURI co-crystalized with ProSeDMA

SM:

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Cryo-EM structure of Saccharolobus solfataricus 30S initiation complex bound to Ss-MAP leaderless mRNA

SM: SPM

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Cryo-EM structure of Saccharolobus solfataricus 30S initiation complex bound to SD mRNA

SM: SPM

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Cryo-EM structure of Saccharolobus solfataricus 30S initiation complex bound to SD mRNA with h44 in up position

SM: SPM

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Cryo-EM structure of Saccharolobus solfataricus 30S initiation complex bound to Ss-aIF2beta leaderless mRNA with h44 in up position

SM: SPM

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Cryo-EM structure of Saccharolobus solfataricus 30S initiation complex bound to Ss-aEF1A-like mRNA

SM: SPM

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Cryo-EM structure of Saccharolobus solfataricus 30S initiation complex bound to Ss-MAP leaderless mRNA with h44 in up position

SM: SPM

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Cryo-EM structure of Saccharolobus solfataricus 30S initiation complex bound to Ss-aIF2beta leaderless mRNA

SM: SPM

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Structure of Candida albicans 80S ribosome in complex with mefloquine (non-rotated state)

SM: YMZ

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The structure of the Candida albicans ribosome with tRNA-fMet, mRNA, and compounds (GEN and MFQ) shows strong density for the A site tRNA

SM: GET

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The structure of the Candida albicans ribosome with tRNA-fMet, mRNA, and compounds (GEN and MFQ) with strong density for the P-site tRNA

SM: GET

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E. coli 70S-TEC complex in delivery state

SM: PHE

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70S ribosome with doublet-decoding tRNASer3 bound to A-site GCA codon

SM: SPM

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70S ribosome with cognate tRNASer3 bound to A-site AGC codon

SM: SPM

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INTERACTION BETWEEN A FLUOROQUINOLONE DERIVATIVE KG022 AND RNAS: EFFECT OF BASE PAIRS 5' ADJACENT TO THE BULGE OUT ESIDUES

SM: 53D

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INTERACTION BETWEEN A FLUOROQUINOLONE DERIVATIVE KG022 AND RNAS: EFFECT OF BASE PAIRS 5' ADJACENT TO THE BULGE OUT RESIDUES

SM: 53D

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INTERACTION BETWEEN A FLUOROQUINOLONE DERIVATIVE KG022 AND RNAS: EFFECT OF BASE PAIRS 5' ADJACENT TO THE BULGE OUT ESIDUES

SM: 53D

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INTERACTION BETWEEN A FLUOROQUINOLONE DERIVATIVE KG022 AND RNAS: EFFECT OF BASE PAIRS 5' ADJACENT TO THE BULGE OUT ESIDUES

SM: 53D

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INTERACTION BETWEEN A FLUOROQUINOLONE DERIVATIVE KG022 AND RNAS: EFFECT OF BASE PAIRS 5' ADJACENT TO THE BULGE OUT ESIDUES

SM: 53D

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pre-mir-125a internal loop in complex with G-clamp

SM:

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CryoEM Structure of the Candida albicans Group I Intron-GMP Complex

SM: 5GP

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CryoEM Structure of the Candida albicans Group I Intron-Compound 11 Complex under Magnesium Condition

SM:

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CryoEM Structure of the Candida albicans Group I Intron-Compound 11 Complex under Calcium Condition

SM:

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Impacts of ribosomal RNA sequence variation on gene expression and phenotype: Cryo-EM structure of the rrsB ribosome (BBB-70S)

SM: ATP

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Impacts of ribosomal RNA sequence variation on gene expression and phenotype: Cryo-EM structure of the rrsH ribosome (HBB-70S)

SM: ATP

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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

Alpharetrovirus

Arabidopsis

Bacillus

Bifidobacterium

Caldanaerobacter

Candida

Candidatus Korobacter

Candidatus Pelagibacter

Clostridium

Cutibacterium

Deinococcus

Didymium

Enterovirus

Escherichia

Faecalibacterium

Fusobacterium

Geobacter

Gloeobacter

Haloarcula

Hepacivirus

Homo

Ideonella

Lacticaseibacillus

Lactococcus

Leishmania

Lentivirus

Listeria

Mesoplasma

Mesorhizobium

Mus

Mycobacterium

Mycolicibacterium

Mycoplasmoides

Nicotiana

Oceanobacillus

Oryctolagus

Pseudomonas

Pylaiella

Pyrobaculum

Ralstonia

Roseobacter

Ruminococcus

Saccharolobus

Saccharomyces

Schaalia

Staphylococcus

Streptococcus

Streptomyces

Sulfobacillus

Sus

Syntrophothermus

Tequatrovirus

Tetrahymena

Thermoanaerobacter

Thermotoga

Thermovirga

Thermus

Tymovirus

Varicellovirus

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

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Dscore

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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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