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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Crystal structure of the L.Lactis YkoY riboswitch bound to cadmium

SM: GTP

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Crystal structure of ykoY-alx riboswitch chimera bound to cadmium

SM: GTP

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Crystal structure of ykoY-mntP riboswitch chimera bound to cadmium

SM: GTP

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Crystal structure of the Thermus thermophilus 70S ribosome in complex with histidyl-CAM and bound to mRNA and A-, P-, and E-site tRNAs at 2.8A resolution

SM: EZG

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Crystal structure of the Thermus thermophilus 70S ribosome in complex with D-histidyl-CAM and bound to protein Y (YfiA) at 2.7A resolution

SM: ARG EZP

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Crystal structure of the Thermus thermophilus 70S ribosome in complex with lysyl-CAM and bound to protein Y (YfiA) at 2.6A resolution

SM: ARG EZM

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Crystal structure of a group II intron lariat with an intact 3' splice site (pre-2s state)

SM: SPM

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G96A mutant of the PRPP riboswitch from T. mathranii bound to ppGpp

SM: G4P GTP

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PRPP riboswitch from T. mathranii bound to PRPP

SM: PRP

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The structure of amicetin bound to the 70S ribosome

SM: ARG

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Structural basis for promiscuous binding and activation of fluorogenic dyes by DIR2s RNA aptamer

SM: G4A

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Structure of the 50S ribosomal subunit from Methicillin Resistant Staphylococcus aureus in complex with the oxazolidinone antibiotic LZD-5

SM: G6V

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Structure of the 50S ribosomal subunit from Methicillin Resistant Staphylococcus aureus in complex with the oxazolidinone antibiotic LZD-6

SM: G6M

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PRPP Riboswitch bound to PRPP, manganese chloride soaked structure

SM: PRP

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PRPP Riboswitch bound to PRPP, iridium-hexamine soaked structure

SM: PRP

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PRPP Riboswitch bound to PRPP, thallium acetate soaked structure

SM: PRP

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PRPP Riboswitch bound to PRPP, native structure

SM: PRP

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ppGpp Riboswitch bound to ppGpp, native structure

SM: G4P

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ppGpp Riboswitch bound to ppGpp, manganese chloride structure

SM: G4P

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ppGpp Riboswitch bound to ppGpp, thallium acetate structure

SM: G4P

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CRYSTAL STRUCTURE OF THE FMN RIBOSWITCH BOUND TO BRX1151 SPLIT RNA

SM: GZ7

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CRYSTAL STRUCTURE OF THE FMN RIBOSWITCH BOUND TO BRX1354 SPLIT RNA

SM: GZG

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CRYSTAL STRUCTURE OF THE FMN RIBOSWITCH BOUND TO BRX1555 SPLIT RNA

SM: GZ4

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Structure of the Thermus thermophilus 30S ribosomal subunit complexed with an unmodifed anticodon stem loop (ASL) of Escherichia coli transfer RNA Arginine 2 (TRNAARG2) bound to an mRNA with an CGU-codon in the A-site and paromomycin

SM: PAR

6e1s

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Crystal structure of a class I PreQ1 riboswitch complexed with a synthetic compound 1: 2-[(dibenzo[b,d]furan-2-yl)oxy]ethan-1-amine

SM: HLV

6e1u

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Crystal structure of a class I PreQ1 riboswitch complexed with a synthetic compound 2: 2-[(dibenzo[b,d]furan-2-yl)oxy]-N,N-dimethylethan-1-amine

SM: HMJ

6e1v

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Crystal structure of a class I PreQ1 riboswitch complexed with a synthetic compound 3: 2-[(9H-carbazol-3-yl)oxy]-N,N-dimethylethan-1-amine

SM: HMV

6e1w

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Crystal structure of a class I PreQ1 riboswitch complexed with PreQ1

SM: HNG

6e81

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Crystal structure of the Corn aptamer in complex with ThT

SM: TFX

6e82

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Crystal structure of the Corn aptamer mutant A14U in complex with ThT

SM: TFX

6e84

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Crystal structure of the Corn aptamer in complex with TO

SM: J0D

6e8t

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Structure of the Mango-III (A10U) aptamer bound to TO1-Biotin

SM: HZG

6e8u

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Structure of the Mango-III (A10U) aptamer bound to TO1-Biotin

SM: HZD

6fz0

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Crystal structure of the metY SAM V riboswitch

SM: SAM

6g7z

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Lariat-capping ribozyme with a shortened DP2 stem loop

SM: MES

6gaw

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Unique features of mammalian mitochondrial translation initiation revealed by cryo-EM. This file contains the complete 55S ribosome.

SM: SPM

6gaz

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Unique features of mammalian mitochondrial translation initiation revealed by cryo-EM. This file contains the 28S ribosomal subunit.

SM: SPM

6gyv

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Lariat-capping ribozyme (circular permutation form)

SM: MES

6gzk

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Solution NMR structure of the tetramethylrhodamine (TMR) aptamer 3 in complex with 5-TAMRA

SM: FH8

6gzr

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Solution NMR structure of the tetramethylrhodamine (TMR) aptamer 3 in complex with 5-TAMRA

SM: FH8

6hag

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The structure of the SAM/SAH-binding riboswitch.

SM: SAH

6hbt

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The structure of the G. violaceus guanidine II riboswitch P2 stem-loop with arcaine

SM: FXQ

6hc5

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The structure of the G. violaceus guanidine II riboswitch P2 stem-loop with audouine

SM: FXT

6hmo

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Solution structure of the RNA duplex formed by the 5'-end of U1snRNA and the 5'-splice site of SMN2 exon7 in complex with the SMN-C5 splicing modifier

SM: GDZ

6i7v

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Ribosomal protein paralogs bL31 and bL36

SM: 1PE PG4

6jbf

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Crystal structure of the bacterial ribosomal decoding site in complex with 4'-deoxy-4'-fluoro neamine analog (axial 4'-F)

SM: V71

6jbg

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Crystal structure of the bacterial ribosomal decoding site in complex with 4'-deoxy-4'-fluoro neamine analog (equatorial 4'-F)

SM: S81

6jji

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Crystal structure of a two-quartet RNA parallel G-quadruplex complexed with the porphyrin TMPyP4 (1:1)

SM: POH

6las

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the wildtype SAM-VI riboswitch bound to SAM

SM: SAM

6lau

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the wildtype SAM-VI riboswitch bound to SAH

SM: GTP SAH

6lax

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the mutant SAM-VI riboswitch (U6C) bound to SAM

SM: SAM

6laz

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the wildtype SAM-VI riboswitch bound to a N-mustard SAM analog M1

SM: E7X

6mkn

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Structure of the Thermus thermophilus 30S ribosomal subunit complexed with an inosine (I34) modified anticodon stem loop (ASL) of Escherichia coli transfer RNA Arginine 2 (TRNAARG2) bound to an mRNA with an CGU-codon in the A-site and paromomycin

SM: PAR

6mpf

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Structure of the Thermus thermophilus 30S ribosomal subunit complexed with a 2-thiocytidine (s2C32) and inosine (I34) modified anticodon stem loop (ASL) of Escherichia coli transfer RNA Arginine 1 (TRNAARG1) bound to an mRNA with an CGC-codon in the A-site and paromomycin

SM: PAR

6mpi

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SM: PAR

6n5k

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Structure of Human pir-miRNA-449c Apical Loop and One-base-pair Fused to the YdaO Riboswitch Scaffold

SM: 2BA

6n5n

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Structure of Human pir-miRNA-208a Apical Loop and One-base-pair Fused to the YdaO Riboswitch Scaffold

SM: 2BA

6n5o

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Structure of Human pir-miRNA-202 Apical Loop and One-base-pair Fused to the YdaO Riboswitch Scaffold

SM: 2BA

6n5p

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Structure of Human pir-miRNA-340 Apical Loop and One-base-pair Fused to the YdaO Riboswitch Scaffold

SM: 2BA

6n5q

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

SM: 2BA

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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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