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

60 120 180

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Structure of the Bacterial Ribosome at 2 Angstrom Resolution

SM: PAR SPM

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High resolution RNA primer complex with guanosine dinucleotide ligand G(5')ppp(5')G

SM: GP3

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LNA modification at 3' end of RNA primer complex with guanosine dinucleotide ligand G(5')ppp(5')G

SM: GP3

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2'-F modification at 3' end of RNA primer complex with guanosine dinucleotide ligand G(5')ppp(5')G

SM: GP3

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FANA modification at 3' end of RNA primer complex with guanosine dinucleotide ligand G(5')ppp(5')G

SM: GP3

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2'-OMe modification at 3' end of RNA primer complex with guanosine dinucleotide ligand G(5')ppp(5')G

SM: GP3

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Crystal structure of Squash RNA aptamer in complex with DFHBI-1T with iridium (III) ions

SM: 2ZY

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Crystal structure of Squash RNA aptamer in complex with DFHBI-1T

SM: 2ZY

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Crystal structure of Squash RNA aptamer in complex with DFHBI-1T

SM: 747

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Spinach variant bound to DFHBI-1T

SM: SPM

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Crystal structure of the Thermus thermophilus 70S ribosome in complex with plazomicin, mRNA and tRNAs

SM: EDS

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ANA modification at 3' end of RNA primer complex with guanosine dinucleotide ligand G(5')ppp(5')G

SM: GP3

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3'-deoxy modification at 3' end of RNA primer complex with guanosine dinucleotide ligand G(5')ppp(5')G

SM: GP3

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TNA modification at 3' end of RNA primer complex with guanosine dinucleotide ligand G(5')ppp(5')G

SM: GP3

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A. baumannii Ribosome-Eravacycline complex: 30S

SM: YQM

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A. baumannii Ribosome-Eravacycline complex: Empty 70S

SM: YQM

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A. baumannii Ribosome-Eravacycline complex: P-site tRNA 70S

SM: YQM

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A. baumannii Ribosome-Eravacycline complex: E-site tRNA 70S

SM: YQM

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Crystal structure of the Thermus thermophilus 70S ribosome in complex with triphenylphosphonium analog of chloramphenicol CAM-C4-TPP and protein Y (YfiA) at 2.80A resolution

SM: ARG

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Crystal structure of r(GU)11G-NMM complex

SM: MMP

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Elongating 70S ribosome complex in a classical pre-translocation (PRE-C) conformation

SM: ATP

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Elongating 70S ribosome complex in a fusidic acid-stalled intermediate state of translocation bound to EF-G(GDP) (INT2)

SM: ATP

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Elongating 70S ribosome complex in a hybrid-H1 pre-translocation (PRE-H1) conformation

SM: ATP

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Elongating 70S ribosome complex in a spectinomycin-stalled intermediate state of translocation bound to EF-G in an active, GTP conformation (INT1)

SM: ATP

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Elongating 70S ribosome complex in a hybrid-H2* pre-translocation (PRE-H2*) conformation

SM: ATP

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Elongating 70S ribosome complex in a post-translocation (POST) conformation

SM: ATP

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55S mammalian mitochondrial ribosome with mtRF1a and P-site tRNAMet

SM: SPM

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55S mammalian mitochondrial ribosome with ICT1 and P site tRNAMet

SM: SPM

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55S mammalian mitochondrial ribosome with mtRRF (pre) and tRNA(P/E)

SM: SPM

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55S mammalian mitochondrial ribosome with tRNA(P/P) and tRNA(E*)

SM: SPM

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Rabbit 80S ribosome stalled close to the mutated SARS-CoV-2 slippery site by a pseudoknot (high resolution)

SM: SPM

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Rabbit 80S ribosome stalled close to the mutated SARS-CoV-2 slippery site by a pseudoknot (classified for pseudoknot)

SM: SPM

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Crystal structure of Chili RNA aptamer in complex with DMHBO+ (Iridium hexammine co-crystallized form)

SM: V5Z

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Crystal structure of Chili RNA aptamer in complex with DMHBO+ (Iridium III hexammine soaking crystal form)

SM: GTP V5Z

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Crystal structure of the Chili RNA aptamer in complex with DMHBI+

SM: GTP SPM V6T

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Crystal structure of the Chili RNA aptamer in complex with DMHBO+

SM: SPM V5Z

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Cryo-EM structure of 70S ribosome stalled with TnaC peptide

SM: PAR

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Mycoplasma pneumoniae 50S subunit of ribosomes in chloramphenicol-treated cells

SM: CLM

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Cryo-EM structure of an Escherichia coli 70S ribosome in complex with elongation factor G and the antibiotic Argyrin B

SM: ATP

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Human mitochondrial ribosome small subunit in complex with IF3, GMPPMP and streptomycin

SM: SPM

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Cryo-EM structure of 70S ribosome stalled with TnaC peptide (control)

SM: CLM

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70S ribosome with A- and P-site tRNAs in chloramphenicol-treated Mycoplasma pneumoniae cells

SM: CLM

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Structure of the 70S ribosome with tRNAs in the classical pre-translocation state and apramycin (C)

SM: AM2

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Structure of the 70S-EF-G-GDP-Pi ribosome complex with tRNAs in hybrid state 1 (H1-EF-G-GDP-Pi)

SM: AM2

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Structure of the 70S-EF-G-GDP ribosome complex with tRNAs in chimeric state 1 (CHI1-EF-G-GDP)

SM: AM2

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Structure of the Candida albicans 80S ribosome in complex with anisomycin

SM: ANM

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Structure of the Candida albicans 80S ribosome in complex with blasticidin s

SM: BLS

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Human mitochondrial ribosome at 2.2 A resolution (bound to partly built tRNAs and mRNA)

SM: SPM

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Human mitochondrial ribosome in complex with mRNA, A/A-, P/P- and E/E-tRNAs at 2.63 A resolution

SM: SPM

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Human mitochondrial ribosome in complex with mRNA, A/P- and P/E-tRNAs at 2.98 A resolution

SM: SPM

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Crystal structure of the Thermus thermophilus 70S ribosome in complex with protein Y, A-site aminoacyl-tRNA analog ACC-PMN, and P-site MTI-tripeptidyl-tRNA analog ACCA-ITM at 2.40A resolution

SM: ARG

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Crystal structure of the Thermus thermophilus 70S ribosome in complex with protein Y, A-site aminoacyl-tRNA analog ACC-PMN, and P-site MAI-tripeptidyl-tRNA analog ACCA-IAM at 2.45A resolution

SM: ARG

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Crystal structure of the Thermus thermophilus 70S ribosome in complex with protein Y, A-site aminoacyl-tRNA analog ACC-PMN, and P-site MFI-tripeptidyl-tRNA analog ACCA-IFM at 2.50A resolution

SM: ARG

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Crystal structure of the Thermus thermophilus 70S ribosome in complex with protein Y, A-site deacylated tRNA analog CACCA, P-site MTI-tripeptidyl-tRNA analog ACCA-ITM, and chloramphenicol at 2.50A resolution

SM: ARG

7rqe

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Crystal structure of the Thermus thermophilus 70S ribosome in complex with protein Y, A-site deacylated tRNA analog CACCA, P-site MAI-tripeptidyl-tRNA analog ACCA-IAM, and chloramphenicol at 2.40A resolution

SM: ARG

7rwr

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An RNA aptamer that decreases flavin redox potential

SM: FMN

7ryf

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A. baumannii Ribosome-TP-6076 complex: P-site tRNA 70S

SM: 80P

7ryg

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A. baumannii Ribosome-TP-6076 complex: E-site tRNA 70S

SM: 80P

7ryh

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A. baumannii Ribosome-TP-6076 complex: Empty 70S

SM: 80P

7s1h

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Wild-type Escherichia coli ribosome with antibiotic linezolid

SM: ZLD

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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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