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 the 50S subunit of the ribosome from Methicillin Resistant Staphylococcus aureus in complex with an isomer of the tedizolid

SM: U7Y

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Structure of Human pir-miRNA-19b-2 Apical Loop and One-base-pair Fused to the YdaO Riboswitch Scaffold

SM: 2BA

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Structure of Human pir-miRNA-300 Apical Loop Fused to the YdaO Riboswitch Scaffold

SM: 2BA

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Fusibacterium ulcerans ZTP riboswitch bound to p-1-pyridinyl AICA

SM: UG1

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Fusibacterium ulcerans ZTP riboswitch bound to m-1-pyridinyl AICA

SM: UG4

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IRES-targeting Small Molecule Inhibits Enterovirus 71 Replication via Allosteric Stabilization of a Ternary Complex

SM: UYS

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Crystal structure of the A2058-unmethylated Thermus thermophilus 70S ribosome in complex with erythromycin and protein Y (YfiA) at 2.55A resolution

SM: ARG

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Class III PreQ1 riboswitch mutant A52G

SM: PRF

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Class III PreQ1 riboswitch mutant A84G

SM: PRF

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Crystal structure of the Thermus thermophilus 70S ribosome in complex with sarecycline, UUC-mRNA, and deacylated P-site tRNA at 2.80A resolution

SM: V7A

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Crystal structure of the Thermus thermophilus 70S ribosome in complex with sarecycline, UAA-mRNA, and deacylated P-site tRNA at 3.00A resolution

SM: V7A

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Structural descriptions of ligand interactions to DNA and RNA quadruplexes folded from the non-coding region of Pseudorabies virus

SM: V8A

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Cryo-EM structure of an Escherichia coli 70S ribosome in complex with antibiotic TetracenomycinX

SM: OCW

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Tetracenomycin X bound to the human ribosome

SM: OCW

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55S mammalian mitochondrial ribosome with mtEFG1 and P site fMet-tRNAMet (POST)

SM: SPM

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55S mammalian mitochondrial ribosome with mtEFG1 and two tRNAMet (TI-POST)

SM: SPM

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Crystal structure of the SAM-SAH riboswitch with SAH

SM: SAH

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Crystal structure of the SAM-SAH riboswitch with SAM

SM: SAM

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Crystal structure of the SAM-SAH riboswitch with AMP.

SM: AMP CBV

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Crystal structure of the SAM-SAH riboswitch with adenosine.

SM: ADN

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Crystal structure of the SAM-SAH riboswitch with AMP

SM: MTA

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Crystal structure of the SAM-SAH riboswitch with decarboxylated SAH

SM: DSH

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Crystal structure of the SAM-SAH riboswitch with SAM from space group P312

SM: SAM

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Acinetobacter baumannii ribosome-amikacin complex - 30S subunit body

SM: AKN

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RNA duplex with a cytosine bulge in complex with berberine

SM: BER

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E. coli 70S containing suppressor tRNA in the A-site stabilized by a Negamycin analogue and P-site tRNA-nascent chain.

SM: SY5

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NMR solution structures of CAG RNA-DB213 binding complex

SM: L94

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Crystal Structure of the Domain1 of NAD+ Riboswitch with nicotinamide adenine dinucleotide (NAD+) and U1A protein

SM: GTP NAD

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Crystal Structure of the Domain1 of NAD+ Riboswitch with nicotinamide adenine dinucleotide (NAD+)

SM: GTP NAD

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Crystal Structure of the Domain1 of NAD+ Riboswitch with adenosine diphosphate (ADP)

SM: ADP GTP

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Crystal Structure of the Domain1 of NAD+ Riboswitch with adenosine triphosphate (ATP)

SM: ATP GTP

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Crystal Structure of the Domain1 of NAD+ Riboswitch with nicotinamide adenine dinucleotide (NAD+), soaked in Mn2+

SM: GTP NAD

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Crystal Structure of the Domain2 of NAD+ Riboswitch with nicotinamide adenine dinucleotide (NAD+)

SM: NAD

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Crystal Structure of the Domain2 of NAD+ Riboswitch with nicotinamide adenine dinucleotide (NAD+), soaked in Mn2+

SM: NAD

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Crystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with mRNA and cognate transfer RNA anticodon stem-loop and sisomicin derivative N1''TFMS bound

SM: HJR

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Crystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with mRNA and cognate transfer RNA anticodon stem-loop and sisomicin derivative N1''AC bound

SM: HJO

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Crystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with mRNA and cognate transfer RNA anticodon stem-loop and sisomicin derivative N1''PyrS bound

SM: HKO

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Crystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with mRNA and cognate transfer RNA anticodon stem-loop and sisomicin derivative N1,3''Bz bound

SM: SIS

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Crystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with mRNA and cognate transfer RNA anticodon stem-loop and sisomicin derivative N1,3''MS bound

SM: SIS

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Crystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with mRNA and cognate transfer RNA anticodon stem-loop and sisomicin derivative N3''MS bound

SM: SIS

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Complex structure of SAM-dependent methyltransferase ribozyme

SM: SAM

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Crystal structure of a class I PreQ1 riboswitch aptamer (ab13-14) complexed with a cognate ligand-derived photoaffinity probe

SM: J0C

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Crystal structure of a class I PreQ1 riboswitch aptamer (wild-type) complexed with a cognate ligand-derived photoaffinity probe

SM: J0C

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Crystal structure of SAM-I riboswitch with the Actinomyces-1 k-turn

SM: SAM

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Crystal structure of the bacterial ribosomal decoding site in complex with G418 and Hg(II)

SM: GET

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Crystal structure of the eukaryotic ribosomal decoding site in complex with G418 and Hg(II)

SM: GET

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RNA duplex containing CC mispairs

SM: SPM

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Crystal structure of xanthine riboswitch with xanthine, iridium hexammine soak

SM: GTP

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Crystal structure of the Pepper aptamer in complex with HBC, iridium hexammine soak

SM: J8F

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Crystal structure of the Pepper aptamer in complex with HBC

SM: J8F

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Crystal structure of the Pepper aptamer in complex with HBC, manganese soak

SM: J8F

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Crystal structure of the Pepper aptamer in complex with HBC, cesium soak

SM: J8F

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Crystal structure of the Pepper aptamer in complex with HBC485

SM: J8L

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Crystal structure of the Pepper aptamer in complex with HBC497

SM: J8O

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Crystal structure of the Pepper aptamer in complex with HBC508

SM: J8R

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Crystal structure of the Pepper aptamer in complex with HBC514

SM: J8U

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Crystal structure of the Pepper aptamer in complex with HBC525

SM: J8X

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Crystal structure of the Pepper aptamer in complex with HBC620

SM: J93

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Interaction between a fluoroquinolone derivative and RNAs with a single bulge

SM: 53D

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Interaction between a fluoroquinolone derivative and RNAs with a single bulge

SM: 53D

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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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