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

862 Complexes found

Complexes per page

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The complete structure of the Mycobacterium smegmatis 70S ribosome

SM: PHE

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iSpinach aptamer

SM: 1TU SPM

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Crystal structure of Gentamicin bound to the yeast 80S ribosome

SM: LLL

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Crystal structure of haemanthamine bound to the 80S ribosome

SM: HN8

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Structure of a guanidine-I riboswitch from S. acidophilus

SM: SPK

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Methicillin sensitive Staphylococcus aureus 70S ribosome

SM: PAR

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RNA primer-template complex with guanosine dinucleotide ligand G(5')pp(5')G

SM: 86S

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RNA primer-template complex with guanosine dinucleotide ligand G(5')ppp(5')G

SM: GP3

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RNA primer-template complex with guanosine dinucleotide G(5')pppp(5')G ligand

SM: 86P

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RNA hairpin structure containing 2-MeImpG monomer analogue and 2-MeImp-oligomer analogue

SM: 8OS

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70S ribosome bound with cognate ternary complex base-paired to A site codon (Structure II)

SM: FME

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70S ribosome bound with cognate ternary complex base-paired to A site codon, closed 30S (Structure III)

SM: FME

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70S ribosome bound with near-cognate ternary complex base-paired to A site codon, open 30S (Structure II-nc)

SM: FME

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70S ribosome bound with near-cognate ternary complex base-paired to A site codon, closed 30S (Structure III-nc)

SM: FME

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RNA duplex with 2-MeImpG analogue bound-one binding site

SM: 8OS

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RNA hairpin structure containing 2-MeImpG analogue bound

SM: 8OS

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Structure of S-GNA dodecamer

SM: SPM

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Co-crystal structure of the fluorogenic RNA Mango

SM: 74G

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Cryo-EM structure of the large ribosomal subunit from Mycobacterium tuberculosis bound with a potent linezolid analog

SM: 917

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Thermus thermophilus 70S ribosome lacking ribosomal protein uS17

SM: ARG

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RNA hairpin structure containing 2-MeImpG analogue bound

SM: 8OS

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RNA hairpin structure containing tetraloop/receptor motif, complexed with 2-MeImpG analogue

SM: 8OS

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RNA hairpin structure containing tetraloop/receptor motif, complexed with 2-MeImpG analogue

SM: 8OS

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Guanidine-II riboswitch P2 hairpin dimer from Pseudomonas aeruginosa

SM: SPM

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Guanidine-II riboswitch P2 hairpin dimer with 5-bromoU substitution from Pseudomonas aeruginosa

SM: SPM

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Crystal structure of the Thermus thermophilus 70S ribosome in complex with madumycin II and bound to mRNA and A-, P- and E-site tRNAs at 2.8A resolution

SM: M2D

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70S ribosome-EF-Tu H84A complex with GppNHp

SM: FME

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70S ribosome-EF-Tu wt complex with GppNHp

SM: FME

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70S ribosome-EF-Tu H84A complex with GTP and cognate tRNA

SM: FME

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70S ribosome-EF-Tu H84A complex with GTP and near-cognate tRNA (Complex C2)

SM: FME

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70S ribosome-EF-Tu H84A complex with GTP and near-cognate tRNA (Complex C3)

SM: FME

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70S ribosome-EF-Tu H84A complex with GTP and near-cognate tRNA (Complex C4)

SM: FME

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Crystal structure of the Thermus thermophilus 70S ribosome in complex with methymycin and bound to mRNA and A-, P- and E-site tRNAs at 2.7A resolution

SM: MT9

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Crystal Structure of 30S ribosomal subunit from Thermus thermophilus

SM: B6M

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Crystal Structure of 30S ribosomal subunit from Thermus thermophilus

SM: B6M

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Crystal Structure of 30S ribosomal subunit from Thermus thermophilus

SM: B6M

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Structural Insight of Flavonoids binding to CAG repeat RNA that causes Huntington's Disease (HD) and Spinocerebellar Ataxia (SCAs)

SM: MYC

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Crystal structure of the Homo Sapiens cytoplasmic ribosomal decoding site in complex with G418

SM: GET

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Crystal structure of the bacterial ribosomal decoding site in complex with 6'-fluoro sisomicin

SM: FSJ

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Crystal structure of the protozoal cytoplasmic ribosomal decoding site in complex with 6'-fluoro sisomicin

SM: FSJ

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Crystal structure of the Homo Sapiens cytoplasmic ribosomal decoding site in complex with G418 (P21212 form)

SM: GET

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Crystal structure of the bacterial A1408me1A-mutant ribosomal decoding site in complex with geneticin

SM: GET

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Crystal structure of the bacterial A1408me1A-mutant ribosomal decoding site in complex with paromomycin

SM: PAR

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Cryo-EM structure of the small subunit of Leishmania ribosome bound to paromomycin

SM: PAR

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Cryo-EM structure of of the large subunit of Leishmania ribosome bound to paromomycin

SM: PAR

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RNA hairpin complex with guanosine dinucleotide ligand G(5')ppp(5')G

SM: GP3

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Crystal structure of a F. nucleatum FMN riboswitch bound to WG-3

SM: DKM

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Crystal Structure of the Mango-II Fluorescent Aptamer Bound to TO1-Biotin

SM: EKJ

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Crystal Structure of the Mango-II Fluorescent Aptamer Bound to TO3-Biotin

SM: EKM

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Crystal Structure of the Mango-II-A22U Fluorescent Aptamer Bound to TO1-Biotin

SM: EKJ

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RNA-imidazolium-bridged intermediate complex, 4h soaking

SM: EQ1

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RNA-activated 2-AIpG monomer complex, 30 min soaking

SM: EQ1

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RNA-activated 2-AIpG monomer complex, 1h soaking

SM: EQ1

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RNA-activated 2-AIpG monomer, 1.5h soaking

SM: EQ1

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RNA-activated 2-AIpG monomer, 3h soaking

SM: EQ4

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Structure of the ribosomal decoding complex at ambient temperature

SM: PAR

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Crystal Structure of 30S ribosomal subunit from Thermus thermophilus in complex with Sisomicin

SM: SIS

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Crystal Structure of 30S ribosomal subunit from Thermus thermophilus

SM: EUS

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Serial Femtosecond X-ray Crystal Structure of 30S ribosomal subunit from Thermus thermophilus in complex with Sisomicin

SM: SIS

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Serial Femtosecond X-ray Crystal Structure of 30S ribosomal subunit from Thermus thermophilus in complex with N1MS

SM: EUS

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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

Arabidopsis

Bacillus

Bifidobacterium

Caldanaerobacter

Candida

Candidatus Koribacter

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

Ralstonia

Roseobacter

Ruminococcus

Saccharomyces

Schaalia

Staphylococcus

Streptococcus

Sulfobacillus

Sus

Syntrophothermus

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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