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

841 Complexes found

Complexes per page

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Structure of the Thermus thermophilus 30S ribosomal subunit complexed with a Valine-ASL with cmo5U in position 34 bound to an mRNA with a GUG-codon in the A-site and paromomycin.

SM: PAR

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Structure of the Thermus thermophilus 30S ribosomal subunit complexed with a Valine-ASL with cmo5U in position 34 bound to an mRNA with a GUC-codon in the A-site and paromomycin.

SM: PAR

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Structure of the Thermus thermophilus 30S ribosomal subunit complexed with a Valine-ASL with cmo5U in position 34 bound to an mRNA with a GUU-codon in the A-site and paromomycin.

SM: PAR

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Structure of the Thermus thermophilus 30S ribosomal subunit complexed with a Valine-ASL with cmo5U in position 34 bound to an mRNA with a GUA-codon in the A-site and paromomycin.

SM: PAR

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Crystal structure of an extended tRNA anticodon stem loop in complex with its cognate mRNA GGGU in the context of the Thermus thermophilus 30S subunit.

SM: PAR

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Crystal structure of an extended tRNA anticodon stem loop in complex with its cognate mRNA UCGU in the context of the Thermus thermophilus 30S subunit.

SM: PAR

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Crystal structure of an extended tRNA anticodon stem loop in complex with its cognate mRNA CGGG in the context of the Thermus thermophilus 30S subunit.

SM: PAR

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Modified uridines with C5-methylene substituents at the first position of the tRNA anticodon stabilize U-G wobble pairing during decoding

SM: PAR

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Modified uridines with C5-methylene substituents at the first position of the tRNA anticodon stabilize U-G wobble pairing during decoding

SM: PAR

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Crystal structure of the SAM-I riboswitch A94G U34 G18U G19U variant in complex with SAM

SM: SAM

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SAM-I riboswitch with a G2nA mutation in the Kink turn in complex with S-adenosylmethionine

SM: SAM

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Crystal structure of a F. nucleatum FMN riboswitch bound to FMN

SM: FMN

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T. tengcongensis glmS ribozyme with G40A mutation, bound to glucosamine-6-phosphate

SM: GLP

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T. tengcongensis glmS ribozyme with G40A mutation, bound to glucosamine-6-phosphate and a substrate RNA with a 2'5'-phosphodiester linkage

SM: GLP

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T. tengcongensis glmS ribozyme bound to glucosamine-6-phosphate and a substrate RNA with a 2'5'-phosphodiester linkage

SM: GLP

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Crystal Structure of the Homo sapiens Mitochondrial Ribosomal Decoding Site in the Presence of SrCl2 (A1555G mutant, Br-derivative)

SM: PAR

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Crystal Structure of the Homo sapiens Mitochondrial Ribosomal Decoding Site in the presence of nonspecifically bound paromomycin (A1555G mutant, Br-derivative)

SM: PAR

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Co-crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit

SM: ANM

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The structure of an enhanced oxazolidinone inhibitor bound to the 50S ribosomal subunit of H. marismortui

SM: SLD

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Structural basis of thiamine pyrophosphate analogues binding to the eukaryotic riboswitch

SM: TPP

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Structure of the eukaryotic TPP-specific riboswitch bound to the antibacterial compound pyrithiamine pyrophosphate

SM: PYI

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Structure of the thiamine pyrophosphate-specific riboswitch bound to oxythiamine pyrophosphate

SM: D2X

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CRYSTAL STRUCTURE OF THE THERMOTOGA MARITIMA LYSINE RIBOSWITCH BOUND TO S-(2-aminoethyl)-L-cysteine

SM: SLZ

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Crystal structure of the Thermotoga maritima lysine riboswitch bound to lysine

SM: 1PE

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Crystallization of the Thermotoga maritima lysine riboswitch bound to lysine, Cs+ Soak

SM: 1PE

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Crystallization of the Thermotoga maritima lysine riboswitch bound to lysine, IRIDIUM HEXAMINE SOAK

SM: 1PE

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Crystallization of the Thermotoga maritima lysine riboswitch bound to homoarginine

SM: 1PE HRG

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Crystallization of the Thermotoga maritima lysine riboswitch bound to N6-1-iminoethyl-L-Lysine

SM: IEL

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The oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect tRNA positioning

SM: ZLD

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Structure of an RNA-2'-deoxyguanosine complex

SM: GNG

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Crystal Structure of the SMK box (SAM-III) Riboswitch with SAM

SM: SAM

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Crystal Structures of the SMK box (SAM-III) Riboswitch with SAH

SM: SAH

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Crystal Structures of the SMK box (SAM-III) Riboswitch with Se-SAM

SM: EEM

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Crystal structure of an in vitro evolved tetracycline aptamer and artificial riboswitch

SM: CTC

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Crystal structure of the FMN riboswitch bound to FMN

SM: FMN

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Crystal structure of the FMN riboswitch bound to FMN, iridium hexamine soak.

SM: FMN

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Crystal structure of the FMn riboswitch bound to FMN, Ba2+ soak.

SM: FMN

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Crystal structure of the FMN riboswitch bound to FMN, Cs+ soak.

SM: FMN

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Crystal structure of the FMN riboswitch bound to FMN, Mn2+ soak.

SM: FMN

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Crystal structure of the FMN riboswitch bound to FMN, cobalt hexammine soak.

SM: FMN

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Crystal structure of the FMN riboswitch bound to FMN, split RNA.

SM: FMN

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Crystal structure of the FMN riboswitch bound to riboflavin.

SM: RBF

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Crystal structure of the FMN riboswitch bound to roseoflavin

SM: RS3

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Crystal structure of guanine riboswitch C74U mutant bound to 6-chloroguanine

SM: 6GU

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Crystal structure of guanine riboswitch bound to 6-O-methylguanine

SM: 6GO

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Cocrystal structure of a class-I preQ1 riboswitch

SM: PRF

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The large ribosomal subunit from Deinococcus radiodurans complexed with Methymycin

SM: MT9

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Co-crystal structure of Tiamulin bound to the large ribosomal subunit

SM: MUL

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Co-crystal structure of Homoharringtonine bound to the large ribosomal subunit

SM: HMT

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Co-crystal structure of Bruceantin bound to the large ribosomal subunit

SM: WIN

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Crystal structure of the G33A mutant Bacillus anthracis glmS ribozyme bound to GlcN6P

SM: GLP

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Crystal structure of the Bacillus anthracis glmS ribozyme bound to MaN6P

SM: 6MN

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Crystal structure of the product Bacillus anthracis glmS ribozyme

SM: GLP

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The structural basis for recognition of the preQ0 metabolite by an unusually small riboswitch aptamer domain

SM: PQ0

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Guanine riboswitch bound to 6-chloroguanine

SM: 6GU

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Crystal structure of the guanine riboswitch C74U mutant bound to 6-O-methylguanine

SM: 6GO

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Guanine riboswitch A21G,U75C mutant bound to 6-chloroguanine

SM: 6GU

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TteSAM-I riboswitch variant A94GU34C bound to sinefungin

SM: SFG

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Crystal structure of the T. tengcongensis SAM-I riboswitch variant U34C/A94G bound with SAH

SM: SAH

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Crystal structure of T. tencongensis SAM-I riboswitch variant A94G/U34 bound with SAM

SM: SAM

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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

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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