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 Human pir-miRNA-320b-2 Apical Loop and One-base-pair Stem Fused to the YdaO Riboswitch Scaffold

SM: 2BA

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Structure of Human pir-miRNA-378a Apical Loop Fused to the YdaO Riboswitch Scaffold

SM: 2BA

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Crystal structure of the Thermus thermophilus 70S ribosome in complex with chloramphenicol and bound to mRNA and A-, P-, and E-site tRNAs at 2.60A resolution

SM: CLM

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Crystal structure of the Thermus thermophilus 70S ribosome in complex with propylamycin and bound to mRNA and A-, P-, and E-site tRNAs at 2.75A resolution

SM: LUJ

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Co-crystal structure of the Fusobacterium ulcerans ZTP riboswitch using an X-ray free-electron laser

SM: AMZ

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Crystal structure of tRNA^ Ala(GGC) bound to cognate 70S A-site

SM: PAR

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Non-rotated ribosome (Structure I)

SM: FME

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Crystal structure of tRNA^ Ala(GGC) bound to the near-cognate 70S A-site

SM: PAR

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Structure of trans-translation inhibitor bound to E. coli 70S ribosome with P site tRNA

SM: KKL

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Crystal structure of tRNA^ Ala(GGC) U32-A38 bound to cognate 70S A site

SM: PAR

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Structural basis for 2'-deoxyguanosine recognition by the 2'-dG-II class of riboswitches

SM: GNG

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E. coli 50S ribosome bound to compound 47

SM: O7S

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E. coli 50S ribosome bound to compound 46

SM: O7V

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E. coli 50S ribosome bound to compound 40q

SM: O7Y

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E. coli 50S ribosome bound to compound 21

SM: O8D

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E. coli 50S ribosome bound to VM2

SM: O8J

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E. coli 50S ribosome bound to compound 40o

SM: O8P

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E. coli 50S ribosome bound to compound 40e

SM: O8S

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E. coli 50S ribosome bound to compound 41q

SM: O8V

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Structure of the iMango-III fluorescent aptamer at room temperature.

SM: OXV

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X-ray crystal structure of the tetrahydrofolate riboswitch aptamer bound to 5-deazatetrahydropterin

SM: T0A

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Crystal structure of seleno-derivative CAG repeats with synthetic CMBL4 compound

SM: J4H

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Structure of a bacterial 50S ribosomal subunit in complex with the novel quinoxolidinone antibiotic cadazolid

SM: JJH

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High-resolution cryo-EM structure of the human 80S ribosome

SM: HMT HYG

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Structure of human mitochondrial 28S ribosome in complex with mitochondrial IF3

SM: SPM

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Structure of human mitochondrial 28S ribosome in complex with mitochondrial IF2 and IF3

SM: SPM

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Erythromycin Resistant Staphylococcus aureus 70S ribosome (delta R88 A89 uL22) in complex with erythromycin.

SM: ERY

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Structure of Oceanobacillus iheyensis group II intron G-mutant (C289G/C358G/G385C) in the presence of K+, Mg2+ and 5'-exon

SM: EPE SPM

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Structure of Oceanobacillus iheyensis group II intron G-mutant (C289G/C358G/G385C) in the presence of Na+, Mg2+ and 5'-exon

SM: EPE

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Structure of Oceanobacillus iheyensis group II intron U-mutant (C289U/C358U/G385A) in the presence of K+, Mg2+ and 5'-exon

SM: EPE SPM

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Structure of Oceanobacillus iheyensis group II intron U-mutant (C289U/C358U/G385A) in the presence of Na+, Mg2+ and 5'-exon

SM: EPE

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Crystal structure of the ADP-binding domain of the NAD+ riboswitch with Adenosine monophosphate (AMP)

SM: AMP

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Crystal structure of the ADP-binding domain of the NAD+ riboswitch with Nicotinamide adenine dinucleotide, reduced (NADH)

SM: NAI

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Crystal structure of the ADP-binding domain of the NAD+ riboswitch with Adenosine diphosphate (ADP)

SM: ADP

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Crystal structure of the ADP-binding domain of the NAD+ riboswitch with Adenosine 5-triphosphate (ATP)

SM: ATP

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Crystal structure of the ADP-binding domain of the NAD+ riboswitch with Cordycepin 5-triphosphate (3-dATP)

SM: 3AT

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Crystal structure of the ADP-binding domain of the NAD+ riboswitch with N6-Methyl-adenosine-5'-triphosphate (m6ATP)

SM: N6E

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Crystal structure of the ADP-binding domain of the NAD+ riboswitch with Nicotinamide adenine dinucleotide (NAD+)

SM: NAD

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Crystal structure of the ADP-binding domain of the NAD+ riboswitch with Adenosine 3-phosphate 5-phosphosulfate (APPS)

SM: PPS

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Crystal structure of the ADP-binding domain of the NAD+ riboswitch with Nicotinamide adenine dinucleotide, reduced (NADH); soaking with Manganese(II) (Mn2+)

SM: NAD

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RNA-monomer complex containing pyrophosphate linkage

SM: EQ4

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RNA duplex, bound with TNA monomer

SM: TG

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RNA hairpin, bound with TNA monomer

SM: TG

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RNA duplex bound with TNA 3'-3' imidazolium dimer

SM: Q1V

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Structure of guanine riboswitch bound to N2-acetyl guanine

SM: Q44

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Guanine riboswitch bound to 8-aminoguanine

SM: ANG

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Guanine riboswitch bound to O6-cyclohexylmethyl guanine

SM: CMG

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Crystal structure of human zinc finger antiviral protein bound to RNA

SM: SPM

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SAM-bound SAM-IV riboswitch

SM: SAM

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Structure of the Mango-III fluorescent aptamer bound to YO3-Biotin

SM: YO3

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Cryo-EM structure of the Acinetobacter baumannii Ribosome: 70S with P-site tRNA

SM: FME

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Co-crystal structure of the fluorogenic Mango-IV homodimer bound to TO1-Biotin

SM: QSA

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Co-crystal structure of the fluorogenic Mango-IV homodimer bound to TO1-Biotin

SM: QW4

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Solution Structure of the Tau pre-mRNA Exon 10 Splicing Regulatory Element Bound to MH5

SM: QSV

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Solution Structure of the Tau pre-mRNA Exon 10 Splicing Regulatory Element Bound to MQC

SM: MQC

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Solution Structure of the Tau pre-mRNA Exon 10 Splicing Regulatory Element Bound to MIP

SM: QSY

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Metabolite-bound PreQ1 riboswitch with Mn2+

SM: PRF

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Structure of the 50S subunit of the ribosome from Methicillin Resistant Staphylococcus aureus in complex with the antibiotic, contezolid

SM: ZC0

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Structure of the 50S subunit of the ribosome from Methicillin Resistant Staphylococcus aureus in complex with the antibiotic, radezolid

SM: RD8

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Structure of the 50S subunit of the ribosome from Methicillin Resistant Staphylococcus aureus in complex with the antibiotic, tedizolid

SM: U7V

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Experimental method

Electron Microscopy

Solution NMR

X-ray

Experimental resolution

Select cutoff values for experimental resolution (Å)

0 : 6

Current selection range: to

Molecular Weight

Select cutoff values for molecular weight of the system complex (kDa)

150 : 1000

150

1000

Current selection range: to

Deposition date

Select cutoff values for the deposition date (years) of the PDB entries

1986 : 2024

1986

2024

Current selection range: to

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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3 : 13086

13086

Current selection range: to

Number of atoms

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0 : 100

100

Current selection range: to

Number of PDB entries

Select cutoff values for the number of PDB entries where the compounds have been resolved

Current selection range: to

Number of interacting chains

Select cutoff values for the number of interacting RNA chains in the pockets

1 : 5

Current selection range: to

Pocket size

Select cutoff values for the number of heavy RNA atoms in the pocket

15.9 : 372

15.9

372

Current selection range: to

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]

0.30000000000000004 : 1.2

0.30000000000000004

1.2

Current selection range: to

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]

0 : 1.2

1.2

Current selection range: to

Exposure

Select cutoff values for the exposure, a score calculated by Schrödinger tool which indicates the degree of exposure to the solvent of the pocket (AU)

0.30000000000000004 : 1

0.30000000000000004

Current selection range: to

Enclosure

Select cutoff values for the enclosure, a score calculated by Schrödinger tool which indicates the degree of buriedness of the pocket (AU)

0.4 : 1

0.4

Current selection range: to

Hydrophobicity

Select cutoff values for the hydrophobicity, a score calculated by Schrödinger tool which indicates the degree of hydrophobicity of the pocket (AU)

0 : 2.1

2.1

Current selection range: to

Hydrophilicity

Select cutoff values for the hydrophilicity, a score calculated by Schrödinger tool which indicates the degree of hydrophilicity of the pocket (AU)

0.30000000000000004 : 2.2

0.30000000000000004

2.2

Current selection range: to

Donor/Acceptor

Select cutoff values for Donor/Acceptor character of the pocket calculated by Schrödinger tool

0.1 : 8.3

0.1

8.3

Current selection range: to

Volume

Select cutoff values for volume of the pocket calculated by Schrödinger tool (Å³)

2 : 1581.3

1581.3

Current selection range: to

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