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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Crystal structure of the E. coli ribosome bound to flopristin.

SM: VIF

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Crystal structure of the E. coli ribosome bound to dalfopristin.

SM: DOL

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Crystal structure of the E. coli ribosome bound to virginiamycin M1.

SM: VIR

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Crystal structure of Anisomycin bound to the yeast 80S ribosome

SM: ANM

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Crystal structure of Geneticin bound to the yeast 80S ribosome

SM: GET

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Crystal structure of Homoharringtonine bound to the yeast 80S ribosome

SM: HMT

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Crystal structure of Lycorine bound to the yeast 80S ribosome

SM: 3KD

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Crystal structure of Verrucarin bound to the yeast 80S ribosome

SM: 3L2

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Crystal structure of Narciclasine bound to the yeast 80S ribosome

SM: 3KF

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Crystal structure of Nagilactone C bound to the yeast 80S ribosome

SM: 3J2

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Crystal structure of Deoxynivalenol bound to the yeast 80S ribosome

SM: 3J6

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Crystal structure of Blasticidin S bound to the yeast 80S ribosome

SM: BLS

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Crystal structure of T-2 toxin bound to the yeast 80S ribosome

SM: ZBA

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Crystal structure of the bacterial ribosome from Escherichia coli in complex with the antibiotic kasugamyin at 3.5A resolution.

SM: KSG

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Structure of the Thermus thermophilus 70S ribosome complexed with mRNA, tRNA and paromomycin

SM: PAR

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Crystal structure of the bacterial ribosome from Escherichia coli in complex with neomycin.

SM: NMY

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Crystal structure of the bacterial ribosome from Escherichia coli in complex with gentamicin.

SM: LLL

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Crystal structure of the bacterial ribosome from Escherichia coli in complex with gentamicin and ribosome recycling factor (RRF).

SM: LLL

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Crystal structure of the bacterial ribosome from Escherichia coli in complex with spectinomycin and neomycin.

SM: NMY

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Structure of the Thermus thermophilus 70S ribosome in complex with mRNA, paromomycin, acylated A-site tRNA, deacylated P-site tRNA, and E-site tRNA.

SM: PAR

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Structure of the Thermus thermophilus 70S ribosome in complex with mRNA, paromomycin, acylated A- and P-site tRNAs, and E-site tRNA.

SM: PAR

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The crystal structure of the 70S ribosome bound to EF-Tu and tRNA

SM: PAR

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Crystal structure of the bacterial ribosome from Escherichia coli in complex with paromomycin and ribosome recycling factor (RRF).

SM: PAR

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Crystal structure of the bacterial ribosome from Escherichia coli in complex with hygromycin B.

SM: HYG

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Crystal structure of the E. coli ribosome bound to chloramphenicol.

SM: CLM

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Crystal structure of the E. coli ribosome bound to clindamycin.

SM: CLY

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Structure of the Thermus thermophilus ribosome complexed with chloramphenicol.

SM: CLM

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The structure of thermorubin in complex with the 70S ribosome from Thermus thermophilus.

SM: T8B

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Crystal structure analysis of ribosomal decoding (near-cognate tRNA-leu complex with paromomycin).

SM: PAR

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Crystal structure analysis of ribosomal decoding (near-cognate tRNA-ttyr complex with paromomycin).

SM: PAR

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Crystal structure of the bacterial ribosome ram mutation G347U.

SM: PAR

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Crystal structure of the bacterial ribosome ram mutation G299A.

SM: PAR

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Crystal Structure of the 70S ribosome with tetracycline.

SM: TAC

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Crystal Structure of the 70S ribosome with tigecycline.

SM: T1C

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Allosteric control of the ribosome by small-molecule antibiotics

SM: NMY

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Crystal Structure of Blasticidin S Bound to Thermus Thermophilus 70S Ribosome.

SM: BLS

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70S ribosome translocation intermediate containing elongation factor EFG/GDP/fusidic acid, mRNA, and tRNAs trapped in the AP/AP pe/E chimeric hybrid state.

SM: NMY

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Crystal structure of the Thermus thermophilus 70S ribosome in complex with negamycin, mRNA and three deacylated tRNAs in the A, P and E sites

SM: NEG

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Crystal structure of Bacillus subtilis cyclic-di-AMP riboswitch ydaO

SM: 2BA

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Crystal structure of Bacillus subtilis cyclic-di-AMP riboswitch ydaO

SM: 2BA

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Crystal structure of the E. coli ribosome bound to negamycin.

SM: NEG

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The crystal structure of the large ribosomal subunit of Staphylococcus aureus in complex with linezolid

SM: ZLD

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The crystal structure of the large ribosomal subunit of Staphylococcus aureus in complex with BC-3205

SM: 3LK EPE

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Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22 in complex with erythromycin

SM: ERY

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4,5-linked aminoglycoside antibiotics regulate the bacterial ribosome by targeting dynamic conformational processes within intersubunit bridge B2

SM: PAR

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Complex of 70S ribosome with tRNA-Tyr and mRNA with A-A mismatch in the first position in the A-site and with antibiotic paromomycin.

SM: PAR

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Complex of 70S ribosome with tRNA-Phe and mRNA with C-A mismatch in the second position in the A-site and with antibiotic paromomycin.

SM: PAR

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Crystal Structure of bactobolin A bound to 70S ribosome-tRNA complex

SM: 3V6 PAR

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Crystal Structure of 30S ribosomal subunit from Thermus thermophilus

SM: PAR

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Crystal Structure of 30S ribosomal subunit from Thermus thermophilus

SM: PAR

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Crystal Structure of 30S ribosomal subunit from Thermus thermophilus

SM: PAR

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Crystal Structure of 30S ribosomal subunit from Thermus thermophilus

SM: PAR

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Crystal structure of the ZMP riboswitch at 2.50 angstrom

SM: AMZ

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Crystal structure of the ZMP riboswitch at 1.80 angstrom

SM: AMZ

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Lactococcus lactis yybP-ykoY Mn riboswitch bound to Mn2+

SM: GTP

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Lactococcus lactis yybP-ykoY Mn riboswitch A41U binding site mutant in presence of Mn2+

SM: GTP

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An Escherichia coli yybP-ykoY Mn riboswitch in the Mn2+-free state

SM: GTP

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Crystal structure of the Thermus thermophilus 70S ribosome with rRNA modifications and bound to protein Y (YfiA) at 2.3A resolution

SM: ARG

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3',3'-cGAMP riboswitch bound with 3',3'-cGAMP

SM: 4BW

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3',3'-cGAMP riboswitch bound with c-di-GMP

SM: C2E

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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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