HARIBOSS

Harnessing RIBOnucleic acid - Small molecules Structures

Compounds
RNA-SM complexes
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Complexes

Complexes

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System Properties

Experimental technique Experimental resolution Molecular weight Deposition date Molecule type Organism With MD simulation With equivalence class

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 RNA environment global RNA family global With binding affinity values Only one non-redundant filter can be selected at a time Non-redundant only Non-redundant only (RNA)

2067 Complexes found

Complexes per page

60 120 180

9v4y

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Crystal structure of Guanine-II riboswitch in complex with 8-aminoguanine

SM: ANG

9v4z

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Crystal structure of Guanine-II riboswitch in complex with 8-oxoguanine

SM: OXG

9v50

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Crystal structure of Guanine-II riboswitch in complex with 8-methylguanine

9v51

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Crystal structure of Guanine-II riboswitch in complex with tetrahydrobiopterin

SM: H4B

9v7n

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Cryo-EM structures of the Azoarcus pre-tRNA(ILE) conformation a undergoing the first-step self-splicing

SM: GMP

9v7o

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Cryo-EM structures of the Azoarcus pre-tRNA(ILE) conformation b undergoing the first-step self-splicing

SM: GMP

9vma

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Cryo-EM structure of substrate-bound DRT9 hexamer complex

SM: DTP

9vmz

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Crystal structure of Broccoli aptamer in with BI

9vuo

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Crystal structure of the DNA/RNA hybrid with Tica

9vxm

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Human mitoribosome in a non-rotated state, with multiple neomycin molecules bound, featuring A/A-site and P/P-site tRNAs

SM: NAD NMY SPM

9vxn

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Human cytosolic ribosome in a rotated state, with multiple neomycin molecules bound, featuring A/P-site and P/E-site tRNAs

SM: NMY

9xe6

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Crimean-Congo hemorrhagic fever virus RNA polymerase containing a 10-bp RNA product and incorporated 2FC

SM: 2KH

9xe7

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Crimean-Congo hemorrhagic fever virus RNA polymerase containing a 10-bp RNA product and incorporated cytidine

SM: 2KH

9xe9

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Crimean-Congo hemorrhagic fever virus RNA polymerase containing a 15-bp RNA product

SM: 2KH

9xec

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Crimean-Congo hemorrhagic fever virus RNA polymerase containing a 9-bp RNA product

SM: 2KH

9yd3

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RNA primer non-enzymatic extension product with RNA substrate

SM: EQ4

9yd4

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RNA primer non-enzymatic extension product with DNA substrate

9ymu

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De novo initial transcribing RNA polymerase with 2-mer RNA and bound CTP / Michaelis complex (RPitc2+CTP)

SM: CTP

9ynp

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Cryo-EM structure of Escherichia coli transcription initiation complex with GpA and pseudouridimycin (PUM)

SM: PUM

9ynq

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Cryo-EM structure of Escherichia coli transcription initiation complex with GpA and des-hydroxy pseudouridimycin (des-hydroxy PUM)

9z2n

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CryoEM structure of human NSUN2(C271A) with SAH cross-linked to tRNA Lys(CTT) (D-arm conformation)

SM: SAH

9z2o

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CryoEM structure of human NSUN2(C271A) with SAH cross-linked to tRNA Lys(CTT) (No D-arm conformation)

SM: SAH

9z2r

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CryoEM structure of human NSUN2 with tRNA Lys(CTT) and SFG (D-arm conformation)

SM: SFG

9z2t

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CryoEM structure of human NSUN2 with tRNA Lys(CTT) and SFG (No D-arm conformation)

SM: SFG

9z2u

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CryoEM structure of human NSUN2(C271A) with SAH cross-linked to tRNA Lys(TTT) (D-arm conformation)

SM: SAH

9z2w

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CryoEM structure of human NSUN2(C271A) with SAH cross-linked to tRNA Lys(TTT) (No D-arm conformation)

SM: SAH

9z3d

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CryoEM structure of human NSUN2(C271A) with SAH cross-linked to a pre-tRNA Leu(CAA) intron

SM: SAH

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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

Alphainfluenzavirus

Alpharetrovirus

Anabaena

Arabidopsis

Archaeoglobus

Azoarcus

Bacillus

Bacteroides

Bandavirus

Betacoronavirus

Betainfluenzavirus

Bifidobacterium

Bombyx

Bos

Brassica

Caenorhabditis

Caldanaerobacter

Candida

Candidatus Korobacter

Candidatus Pelagibacter

Carnobacterium

Chlamydomonas

Clostridium

Coxiella

Cutibacterium

Cypovirus

Deinococcus

Desulfonema

Didymium

Entamoeba

Enterococcus

Enterovirus

Escherichia

Faecalibacterium

Francisella

Fusobacterium

Geobacter

Giardia

Gloeobacter

Halalkalibacterium (ex Joshi et al. 2022)

Haloarcula

Henipavirus

Hepacivirus

Homo

Ideonella

Klebsiella

Kluyveromyces

Lacticaseibacillus

Lactococcus

Leishmania

Lentivirus

Listeria

Mammarenavirus

Mesoplasma

Mesorhizobium

Mus

Mycobacterium

Mycolicibacterium

Mycoplasmoides

Neurospora

Nicotiana

Oceanobacillus

Orthobunyavirus

Orthoflavivirus

Orthonairovirus

Orthopneumovirus

Orthoreovirus

Oryctolagus

Paenibacillus

Plasmodium

Porphyromonas

Pseudomonas

Pylaiella

Pyrobaculum

Ralstonia

Rauchvirus

Roseobacter

Rotavirus

Ruminococcus

Saccharolobus

Saccharomyces

Schaalia

Segatella

Solanum

Staphylococcus

Streptococcus

Streptomyces

Sulfobacillus

Sulfolobus

Sus

Syntrophothermus

Taeniopygia

Tequatrovirus

Teseptimavirus

Tetrahymena

Thermoanaerobacter

Thermochaetoides

Thermotoga

Thermovirga

Thermus

Thogotovirus

Tilapinevirus

Tribolium

Trichoplusia

Triticum

Trypanosoma

Tymovirus

Varicellovirus

Vesiculovirus

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

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]

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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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RNA environment global

RNA

RNA/DNA

RNA/DNA/Protein

RNA/Other

RNA/Protein

RNA family global

RNA/DNA_hybrid

TAR_rna

aptamer_rna

mRNA

multiple

rRNA

riboswitch

ribozyme

snRNA

sre_rna

synthetic construct

tRNA

telomerase_RNA

unknown

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