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

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Crystal Structure Of Erythromycin Bound To The G2099A Mutant 50S Ribosomal Subunit Of Haloarcula Marismortui

SM: ERY

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Crystal Structure Of Clindamycin Bound To The G2099A Mutant 50S Ribosomal Subunit Of Haloarcula Marismortui

SM: CLY

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Crystal structure of the Diels-Alder ribozyme complexed with the product of the reaction between N-pentylmaleimide and covalently attached 9-hydroxymethylanthracene

SM: DAI

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Crystal structure of selenium-modified Diels-Alder ribozyme complexed with the product of the reaction between N-pentylmaleimide and covalently attached 9-hydroxymethylanthracene

SM: DAI

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Crystal Structure of Apramycin bound to a Ribosomal RNA A site oligonucleotide

SM: AM2

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Crystal structure of a complex of the ribosome large subunit with rapamycin

SM: RAP

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Molecular Recognition of RNA by Neomycin and a Restricted Neomycin Derivative

SM: CNY

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Molecular Recognition of RNA by Neomycin and a Restricted Neomycin Derivative

SM: NMY

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Class I GTP aptamer

SM: GTP

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Complex Between Paromomycin Derivative JS5-39 and the 16S-Rrna A-Site.

SM: JS5

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Complex Between Paromomycin derivative JS4 and the 16S-Rrna A Site

SM: JS4

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Structure of the Arabidopsis thaliana thiamine pyrophosphate riboswitch with its regulatory ligand

SM: TPP

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Complex between Kanamycin A and the 16S-Rrna A Site.

SM: KAN

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Complex between Lividomycin A and the 16S-Rrna A Site

SM: LIV

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Complex Between Gentamicin C1A and the 16S-RRNA A-Site

SM: LLL

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Complex Between Neomycin B and the 16S-RRNA A-Site

SM: NMY

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Complex Between Neamine and the 16S-RRNA A-Site

SM: XXX

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A-site RNA in complex with neamine

SM: XXX

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Asite RNA + designer antibiotic

SM: AB9

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Asite RNA + designer antibiotic

SM: AB6

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30S ribosome + designer antibiotic

SM: AB9 D2C

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Crystal Structure of the Homo sapiens Cytoplasmic Ribosomal Decoding Site complexed with Apramycin

SM: AM2

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Crystal structure of thiamine pyrophosphate-specific riboswitch in complex with thiamine pyrophosphate

SM: TPP

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Structure of the S-adenosylmethionine riboswitch mRNA regulatory element

SM: SAM

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Crystal structure of kasugamycin bound to the 30S ribosomal subunit

SM: KSG

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Pre-cleavage state of the Thermoanaerobacter tengcongensis glmS ribozyme bound to glucose-6-phosphate

SM: G6P

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Crystal structure of an E. coli thi-box riboswitch bound to thiamine pyrophosphate, manganese ions

SM: TPP

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Crystal structure of an E. coli thi-box riboswitch bound to thiamine pyrophosphate, barium ions

SM: TPP

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Crystal structure of an E. coli thi-box riboswitch bound to thiamine monophosphate

SM: TPS

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Crystal structure of an E. coli thi-box riboswitch bound to benfotiamine

SM: BFT

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Crystal structure of an E. coli thi-box riboswitch bound to pyrithiamine

SM: 218

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guanidino neomycin B recognition of an HIV-1 RNA helix

SM: G0B

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Solution structure and thermodynamics of 2',5' RNA intercalation

SM: PRL

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Structural basis for stabilization of the tau pre-mRNA splicing regulatory element by Novantrone (Mitoxantrone)

SM: MIX

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Inhibitor Induced Structural Change in the HCV IRES Domain IIa RNA

SM: ISH

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Inhibitor Induced Structural Change in the HCV IRES Domain IIa RNA

SM: ISI

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NMR structure of stem-loop 4 from the human 7SK snRNA in complex with arginine

SM: ARG

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Solution NMR Structure of the 27 nucleotide engineered neomycin sensing riboswitch RNA-ribostmycin complex

SM: RIO

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Solution structure of a preQ1 riboswitch (Class I) aptamer bound to preQ1

SM: PRF

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Structure of the HIV-1 frameshift site RNA bound to a small molecule inhibitor of viral replication

SM: L94

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Solution structure of small molecule-influenza RNA complex

SM: 0EC

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NMR structure of E. coli ribosomela decoding site with apramycin

SM: AM2

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Solution NMR structure of a preQ1 Class II riboswitch from Streptococcus pneumoniae

SM: PRF

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Solution NMR-structure of the neomycin sensing riboswitch RNA bound to paromomycin

SM: PAR

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Solution NMR Structure of the 27 nucleotide engineered neomycin sensing riboswitch RNA-ribostamycin complex

SM: RIO

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Structural investigation of the GlmS ribozyme bound to its catalytic cofactor

SM: GLP

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Crystal Structure of the Homo sapiens Cytoplasmic Ribosomal Decoding Site complexed with paromamine derivative NB33

SM: N33

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Crystal Structure of the Homo sapiens Cytoplasmic Ribosomal Decoding Site in presence of paromomycin

SM: PAR

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Crystal Structure of the Prokaryotic Ribosomal Decoding Site Complexed with Paromamine Derivative NB30

SM: N30

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Crystal Structure of the Homo sapiens Cytoplasmic Ribosomal Decoding Site in Presence of Paromamine Derivative NB30

SM: SPM

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Structure of 23S rRNA of the large ribosomal subunit from Deinococcus radiodurans in complex with the macrolide erythromycylamine

SM: ERN

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Structure of 23S rRNA of the large ribosomal subunit from Deinococcus radiodurans in complex with the macrolide josamycin

SM: JOS

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Structure of the 23S rRNA of the large ribosomal subunit from Deinococcus Radiodurans in complex with the macrolide RU-69874

SM: RU6

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1.5 A X-ray crystal structure of Apramycin complex with RNA fragment GGCGUCGCUAGUACCG/GGUACUAAAAGUCGCCC containing the human ribosomal decoding A site: RNA construct with 3'-overhang

SM: AM2

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1.8 A X-ray crystal structure of Apramycin complex with RNA fragment GGGCGUCGCUAGUACC/CGGUACUAAAAGUCGCC containing the human ribosomal decoding A site: RNA construct with 5'-overhang

SM: AM2

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The crystal structure of the large ribosomal subunit from Deinococcus radiodurans complexed with the pleuromutilin derivative SB-280080

SM: G80

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The crystal structure of the large ribosomal subunit from Deinococcus radiodurans complexed with the pleuromutilin derivative retapamulin (SB-275833)

SM: G34

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Crystal structure of the bacterial ribosomal decoding site complexed with aminoglycoside containing the L-HABA group

SM: LHA

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SAM-II riboswitch bound to S-adenosylmethionine

SM: SAM

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RESTRAINED REFINEMENT OF TWO CRYSTALLINE FORMS OF YEAST ASPARTIC ACID AND PHENYLALANINE TRANSFER RNA CRYSTALS

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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