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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Cutibacterium acnes 30S ribosomal subunit with Sarecycline bound, head domain only in the local refined map

SM: V7A

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Crystal structure of theophylline aptamer in complex with theophylline

SM: TEP

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Crystal structure of theophylline aptamer in complex with TAL3

SM: QB3

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Crystal structure of theophylline aptamer in complex with TAL2

SM: QAX

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Crystal structure of theophylline aptamer in complex with TAL1

SM: QIJ

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Crystal structure of theophylline aptamer in complex with TAL4

SM: QEU

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E. coli 50S ribosome bound to compound streptogramin A analog 3142

SM: UE6

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E. coli 50S ribosome bound to compound streptogramin A analog 3146

SM: UEC

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E. coli 50S ribosome bound to compound streptogramin A analog 3336

SM: UI0

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E. coli 50S ribosome bound to antibiotic analog SLC09

SM: UI9

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E. coli 50S ribosome bound to antibiotic analog SLC30

SM: UIF

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E. coli 50S ribosome bound to antibiotic analog SLC31

SM: UH0

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E. coli 70S ribosome with A-loop mutations U2554C and U2555C

SM: PAR SPM

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Escherichia coli 70S ribosome bound to thermorubin, deacylated P-site tRNAfMet and aminoacylated A-site Phe-tRNA

SM: T8B

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Composite 70S ribosome structure for "Atomistic simulations of the E. coli ribosome provide selection criteria for translationally active substrates

SM: PAR SPM

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Crystal structure of the Thermus thermophilus 70S ribosome in complex with amikacin, mRNA, and A-, P-, and E-site tRNAs

SM: AKN

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Crystal structure of the Thermus thermophilus 70S ribosome in complex with kanamycin, mRNA, and A-, P-, and E-site tRNAs

SM: KAN

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Structure of Beetroot dimer bound to DFAME

SM: X5R

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Structure of Beetroot dimer bound to DFHO

SM: 747

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Beetroot dimer bound to ThT

SM: TFX

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Wobble Beetroot (A16U-U38G) dimer bound to DFHO

SM: 747

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Apo structure of the TPP riboswitch aptamer domain

SM: PG4

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Crystal structure of the Thermus thermophilus 70S ribosome in complex with protein Y, hygromycin A, and erythromycin at 2.50A resolution

SM: ARG

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Crystal structure of the Thermus thermophilus 70S ribosome in complex with protein Y, hygromycin A, and azithromycin at 2.50A resolution

SM: ARG

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Crystal structure of the Thermus thermophilus 70S ribosome in complex with protein Y, hygromycin A, and telithromycin at 2.60A resolution

SM: ARG

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Crystal structure of the A2058-N6-dimethylated Thermus thermophilus 70S ribosome in complex with protein Y, hygromycin A, and erythromycin at 2.45A resolution

SM: ARG HGR

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Crystal structure of the A2058-N6-dimethylated Thermus thermophilus 70S ribosome in complex with protein Y, hygromycin A, and azithromycin at 2.65A resolution

SM: ARG

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Crystal structure of the A2058-N6-dimethylated Thermus thermophilus 70S ribosome in complex with protein Y, hygromycin A, and telithromycin at 2.35A resolution

SM: ARG

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E. coli 70S ribosome with an improved MS2 tag inserted in H98

SM: FME

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Class I type III preQ1 riboswitch from E. coli

SM: PRF

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Cryo-EM consensus structure of Escherichia coli que-PEC (paused elongation complex) RNA Polymerase plus preQ1 ligand

SM: PRF

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mRNA decoding in human is kinetically and structurally distinct from bacteria (IC state)

SM: ANM

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mRNA decoding in human is kinetically and structurally distinct from bacteria (GA state)

SM: ANM

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mRNA decoding in human is kinetically and structurally distinct from bacteria (CR state)

SM: ANM

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mRNA decoding in human is kinetically and structurally distinct from bacteria (AC state)

SM: ANM

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mRNA decoding in human is kinetically and structurally distinct from bacteria (GA state 2)

SM: HMT

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Structure of WT E.coli 70S ribosome complexed with mRNA, P-site fMet-NH-tRNAfMet and A-site ortho-aminobenzoic acid charged NH-tRNAPhe

SM: PAR

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Structure of WT E.coli ribosome 50S subunit with complexed with mRNA, P-site fMet-NH-tRNAfMet and A-site meta-aminobenzoic acid charged NH-tRNAPhe

SM: SPM

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Cryo-EM structure of 3DVA component 0 of Escherichia coli que-PEC (paused elongation complex) RNA Polymerase plus preQ1 ligand

SM: PRF

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Structure of the Escherichia coli 70S ribosome in complex with EF-Tu and Ile-tRNAIle(LAU) bound to the near-cognate AUG codon (Structure II)

SM: PAR

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Structure of the Escherichia coli 70S ribosome in complex with A-site tRNAIle(LAU) bound to the cognate AUA codon (Structure III)

SM: PAR

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Cryo-EM structure of 3DVA component 1 of Escherichia coli que-PEC (paused elongation complex) RNA Polymerase plus preQ1 ligand

SM: PRF

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mRNA decoding in human is kinetically and structurally distinct from bacteria (Consensus LSU focused refined structure)

SM: ANM

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Crystal structure of NAD+ -II riboswitch in complex with NAD+

SM: NAD

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Crystal structure of NAD+ -II riboswitch in complex with NMN

SM: NMN

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

SM: NMN

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Crystal structure of NAD-II riboswitch (two strands) with NR

SM: NNR

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Crystal structure of NAD-II riboswitch (single strand) with NMN

SM: NMN

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Crystal structure of NAD-II riboswitch (single strand) with NAD

SM: NAD NMN

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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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Ternary complex of translating ribosome, NAC and METAP1

SM: SPM

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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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