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

60 120 180

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GpppA dinucleotide binding to RNA CU template

SM: G3A

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RNA duplex bound with GMP and AMP monomers

SM: 5GP

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RNA UU template binding to AMP monomer

SM: AMP

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RNA duplex bound with imidazolium bridged GA dinucleotide

SM: WZW

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Crystal structure of RNA device 43 truncation mutant 3 (U100C), holo state

SM: TAC

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Cryo-EM structure of the Escherichia coli 70S ribosome in complex with amikacin, mRNA, and A-, P-, and E-site tRNAs

SM: AKN

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Cryo-EM structure of RNA device 43, holo state

SM: TAC

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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 formyl-MAI-tripeptidyl-tRNA analog ACCA-IAMf at 2.65A 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 formyl-MFI-tripeptidyl-tRNA analog ACCA-IFMf at 2.60A resolution

SM: ARG

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Class III PreQ1 riboswitch double mutant U8C/A85G

SM: PRF

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Structure of Mango II aptamer bound to T01-6A

SM: VK0

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Structure of Mango II aptamer bound to T01-6A-B

SM: VKI

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Structure of Mango II variant aptamer bound to T01-6A-B

SM: VLR

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Structure of Mango II variant aptamer bound to T01-7M-B

SM: W6F

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Structure of Mango II variant2 aptamer bound to T01-6A

SM: VK0

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In situ HHT and CHX treated human 80S ribosome with EBP1 (consensus map)

SM: HMT

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yjdF riboswitch from R. gauvreauii in complex with chelerythrine bound to Fab BL3-6 S97N

SM: CTI

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yjdF riboswitch from R. gauvreauii in complex with proflavine bound to Fab BL3-6 S97N

SM: PRL

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Magnesium catalyzed primer extension product with 14mer primer and mixed phosphorothioate activated G monomer

SM: DGP

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Cadmium catalyzed primer extension product with 14mer primer and mixed phosphorothioate activated G monomer

SM: DGP

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Structure of Mycobacterium smegmatis 50S ribosomal subunit bound to HflX and erythromycin:50S-HflX-B-Ery

SM: ERY

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Class III PreQ1 riboswitch mutant delta84

SM: PRF

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Structure of S. odontolytica ZTP riboswitch bound to m-1-pyridinyl-AICA

SM: UG4

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Structure of Mycobacterium smegmatis 50S ribosomal subunit bound to HflX and chloramphenicol:50S-HflX-B-Clm

SM: CLM

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Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with macrolone MCX-128 and protein Y at 2.35A resolution

SM: ARG

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

SM: ARG CPF

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Structure of S. odontolytica ZTP riboswitch bound to m-1-pyridinyl-AICA

SM:

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Mango II bound to 365A-061

SM:

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Mango II bound to 365A-084

SM:

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Mango II bound to 365A-087

SM:

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Mango II bound to 365A-088

SM:

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Cryo-EM structure of the human 80S ribosome with Tigecycline, E-tRNA, SERBP1 and eEF2

SM: T1C

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Cryo-EM structure of the human 80S ribosome with Tigecycline, e-tRNA and CCDC124 (40S head Swivelled)

SM: T1C

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Cryo-EM structure of the human 80S ribosome with Tigecycline, E-tRNA and P-tRNA

SM: T1C

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Cryo-EM structure of the human 55S mitoribosome with 5um Tigecycline

SM: T1C

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Cryo-EM structure of the human 39S mitoribosome with 5uM Tigecycline

SM: T1C

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Cryo-EM structure of the human 55S mitoribosome with 10uM Tigecycline

SM: T1C

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Cryo-EM structure of the human 39S mitoribosome with 10uM Tigecycline

SM: T1C

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Crystal structure of THF-II riboswitch with THF and soaked with Ir

SM: SPM THG

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Crystal structure of folE riboswitch with DHF

SM: DHF SPM

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Crystal structure of folE riboswitch with DHN

SM: NPR SPM

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Crystal structure of folE riboswitch with BH4

SM: H4B SPM

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Crystal structure of folE riboswitch with Guanine

SM: SPM

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Crystal structure of folE riboswitch with 8-CH3 Guanine

SM: SPM

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Crystal structure of folE riboswitch with 8-N Guanine

SM: SPM

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Crystal structure of folE riboswitch with 8-NH2 Guanine

SM: ANG SPM

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Crystal structure of THF-II riboswitch with THF and soaked with Ir

SM: SPM THG

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Crystal structure of a class I PreQ1 riboswitch complexed with a synthetic compound

SM:

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Crystal structure of a class I PreQ1 riboswitch complexed with a synthetic compound

SM:

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RNA duplex containing Formamide

SM: SPM

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Cryo-EM structure of the human 80S ribosome with 100 um Tigecycline

SM: T1C

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Solution structure of the complex of naphthyridine-azaquinolone and an RNA with ACG/AUA motif

SM: NAZ

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Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with berberine analog of chloramphenicol CAM-BER, mRNA, deacylated A- and E-site tRNAphe, and deacylated P-site tRNAmet at 2.80A resolution

SM:

9bun

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RhoBAST aptamer RNA in complex with 5(6)-carboxytetramethylrhodamine

SM: FH8

9bzc

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Cocrystal structure of Clostridium beijerinckii ZTP riboswitch with ZMP and Cs

SM: AMZ

9c4g

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Cutibacterium acnes 50S ribosomal subunit with Clindamycin bound

SM: CLY

9c6k

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Cryo-EM structure of the TPP riboswitch embedded in an RNA scaffold bound to thiamine pyrophosphate

SM: TPP

9cn3

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Human 39S mitoribosome in complex with antibiotic Linezolid

SM: ZLD

9cpd

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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: MQC

9cpg

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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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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

Select cutoff values for the SiteScore, ligandability score calcultated by Schrödinger tool. Below 0.8 the pocket is considered non-drug binding site, between 0.8 and 1.0 a potential drug binding site, and above 1.0 a promising binding site [TODO add ref]

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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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