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

Complexes per page

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A new fluorescent RNA aptamer bound with N, manganese soak

SM: NI4

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Crystal structure of NAD-II riboswitch (two strands) with NMN at 1.67 angstrom

SM: NMN

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Interaction between a fluoroquinolone derivative KG022 and RNAs: effect of base pairs 3' adjacent to the bulge out residues

SM: 53D

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Interaction between a fluoroquinolone derivative KG022 and RNAs: effect of base pairs 3' adjacent to the bulge out residues

SM: 53D

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Interaction between a fluoroquinolone derivative KG022 and RNAs: effect of base pairs 3' adjacent to the bulge out residues

SM: 53D

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Interaction between a fluoroquinolone derivative KG022 and RNAs: effect of base pairs 3' adjacent to the bulge out residues

SM: 53D

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The Tet-S1 state of G264A mutated Tetrahymena group I intron with 6nt 3'/5'-exon and 2-aminopurine nucleoside

SM: OJI

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Dibekacin-bound E.coli 70S ribosome in the PURE system

SM: 84D SPM

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Arbekacin-bound E.coli 70S ribosome in the PURE system

SM: 84G SPM

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Dibekacin-added human 80S ribosome

SM: 84D

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Arbekacin-added human 80S ribosome

SM: 84G

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Crystal structure of RhoBAST complexed with TMR-DN

SM: V8C

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Cryo-EM structure of the human 55S mitoribosome with Tigecycline

SM: T1C

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Cryo-EM structure of the human 39S mitoribosome with Tigecycline

SM: T1C

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Cryo-EM structure of the human 80S ribosome with Tigecycline

SM: T1C

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Crystal structure of Broccoli aptamer with DFHBI-1T

SM: 2ZY

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Cryo-EM structure of the yeast 80S ribosome with tigecycline, Not5 and P-site tRNA

SM: T1C

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Crystal structure of Red Broccoli aptamer with OBI

SM:

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Crystal structure of 2'-dG-III riboswitch with 2'-dG

SM: GNG

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Crystal structure of 2'-dG-III riboswitch with guanosine

SM: GMP

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Crystal structure of the Candida albicans 80S ribosome in complex with Paromomycin (250uM)

SM: PAR

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Structure of Candida albicans 80S ribosome in complex with mefloquine

SM: YMZ

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Crystal structure of the Candida albicans 80S ribosome in complex with Paromomycin (500umol)

SM: PAR

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Crystal structure of the Candida albicans 80S ribosome in complex with Paromomycin (2mM)

SM: PAR

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Crystal structure of the Candida albicans 80S ribosome in complex with geneticin G418 (rotated state)

SM: GET

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Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+ and intronistat B

SM: EPE SPM VTE

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Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+ and ARN25850

SM: EPE SPM VTR

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Structure of Oceanobacillus iheyensis group II intron post first step of splicing in the presence of K+, Mg2+ and intronistat B

SM: EPE SPM

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Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+, 5'-exon, and intronistat B after 2h30 soaking

SM: EPE SPM VTE

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Structure of Oceanobacillus iheyensis group II intron in the presence of Na+, Mg2+ and intronistat B

SM: GDE

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E167K RF2 on E. coli 70S release complex with UGG (Structure I)

SM: SPM

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E167K RF2 on E. coli 70S release complex with UGG (Structure II)

SM: SPM

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E167K RF2 on E. coli 70S release complex with UGG (Structure III)

SM: SPM

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Ternary complex of translating ribosome, NAC and METAP1

SM: SPM

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Mycoplasma pneumoniae 70S ribosome in chloramphenicol-treated cells

SM: SPM

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Mycoplasma pneumoniae 70S ribosome with second S4 protein on large subunit

SM: SPM

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Mycoplasma pneumoniae large ribosomal subunit in chloramphenicol-treated cells

SM: SPM

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Escherichia coli paused disome complex (queueing 70S non-rotated closed PRE state)

SM: ATP

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Structure of arbekacin bound Escherichia coli 70S ribosome

SM: 84G

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E167K RF2 on E. coli 70S release complex with UAA

SM: SPM

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Crystal structure of RNA G2C4 repeats in complex with small synthetic molecule ANP77

SM: W53

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mt-SSU assembly intermediate in GTPBP8 knock-out cells, state 1

SM: SPM

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mt-SSU assembly intermediate in GTPBP8 knock-out cells, state 3

SM: SPM

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mt-SSU in GTPBP8 knock-out cells, state 4

SM: SPM

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Human 60S ribosomal subunit

SM: SPM

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Solution structure of Risdiplam bound to the RNA duplex formed upon 5'-splice site recognition

SM: Y59

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Solution structure of branaplam bound to the RNA duplex formed upon 5'-splice site recognition

SM: Y53

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Solution structure of SMN-CX bound to the RNA helix formed upon SMN2 exon7 5'-splice site recognition

SM: YB3

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Human mitochondrial ribosome in complex with antibiotic tigecycline

SM: T1C

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Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+ and 5'-exon

SM: EPE

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Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+, 5'-exon, and intronistat B after 1h soaking

SM: VTE

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Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+, 5'-exon, and ARN25850 after 1h soaking

SM:

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Structure of Oceanobacillus iheyensis group II intron in the presence of Na+, Mg2+, and ARN25850

SM: VTR

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Structure of Oceanobacillus iheyensis group II intron in the presence of Li+ and Mg2+

SM: EPE

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Structure of Oceanobacillus iheyensis group II intron in the presence of Li+, Mg2+, and intronistat B

SM: VTE

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Structure of Oceanobacillus iheyensis group II intron in the presence of Li+, Mg2+, and ARN25850

SM: EPE VTR

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CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME WITH A/P/E-site tRNA AND mRNA : PARENTAL STRAIN

SM:

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YlmH bound to PtRNA-50S

SM: CLM

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RNA duplex bound with GpppA dinucleotide ligand

SM: G3A

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GpppA dinucleotide ligand binding to RNA UC template

SM: G3A

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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

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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