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

1122 Complexes found

Complexes per page

60 120 180

filters used: RNA environment global: RNA

9ps0

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In situ structure of the human mitoribosome in the A/P-P/E state from TACO1-knockout cells

9ps7

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In situ structure of the human mitoribosome in the A/T-P-E state from TACO1-knockout cells

9psi

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In situ structure of the human mitoribosome in the A-P-E state from TACO1-knockout cells

9psm

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In situ structure of the human mitoribosome in the A/P-P/E state

9q0i

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Structure of dsRNA 16mer containing 4'-C-methyladenosine

SM: SPM

9qqa

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Ternary complex of translating ribosome, NAC and NMT1

SM: SPM

9qqb

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Quaternary complex of a translating ribosome, NAC, NMT1, and NatA

SM: SPM

9rbf

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Structure of a stalled E. coli 70S RNC-NuoK-86 in complex with the membrane protein insertase SecYEG-YidC

SM: SPM

9rja

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Manikomycin bound to the Escherichia coli 70S ribosome

SM: PAR

9ror

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Assembly intermediate of human mitochondrial ribosome small subunit bound to METTL15 and RBFA (Outward conformation) (State M3)

9rot

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Assembly intermediate of human mitochondrial ribosome small subunit bound to METTL15, RBFA, and mtIF2 (State M2.1)

9rov

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Assembly intermediate of human mitochondrial ribosome small subunit bound to METTL15 and RBFA (Inward conformation) (State M2)

9rpv

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Structure of the ZAK-bound human disome

SM: ANM

9rtu

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Structure of the 70S-EF-G(P610L)-GDP-Pi ribosome complex with tRNAs in hybrid state 1 (H1-EF-G(P610L)-GDP-Pi)

9rtv

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Structure of the 70S-EF-G(P610L)-GDP-Pi ribosome complex with tRNAs in hybrid state 2 (H2-EF-G(P610L)-GDP-Pi)

9ru7

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WT-HEK 80S ribosome bound to Kozak mRNA (WT-Kozak)

SM: HYG

9ru8

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WT-HEK 80S ribosome bound to TISU mRNA (WT-TISU)

SM: HYG

9ru9

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RPS26dC HEK mutant 80S ribosome bound to Kozak mRNA (RPS26dC-Kozak)

9ruc

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WT-HEK 80S ribosome bound to H2B mRNA (WT-H2B)

SM: HYG

9slg

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Doxycycline Bound E. coli Ribosome with Rearranged Peptidyl Transferase Centre

SM: DXT

9spf

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CRYO-EM STRUCTURE OF HUMAN 80S RIBOSOME WITH A/P/E-SITE TRNA AND MRNA CONTAINING N1-METHYLPSEUDOURIDINE

SM: HYG

9spi

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CRYO-EM STRUCTURE OF HUMAN 80S RIBOSOME WITH A/P/E-SITE TRNA AND MRNA CONTAINING URIDINE

SM: HYG

9sx2

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30S Doxycycline Bound E. coli Ribosome

SM: DXT

9t5x

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Structure of a stalled E. coli 70S RNC-NuoK-70 in complex with the membrane protein insertase SecYEG-YidC

SM: SPM

9t61

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Doxycycline Bound C. burnetii 30S Ribosome

SM: DXT

9t6h

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Cryo-EM structure of the 70S ribosome from Francisella tularensis bound to antibiotics chloramphenicol and gentamicin

9tey

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DalDro bound to the terminating Escherichia coli 70S ribosome

SM: SPM

9tez

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DalDroS bound to the Escherichia coli 50S ribosomal subunit

SM: SPM

9uw0

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Crystal structure of 2'-dG-III riboswitch with Guanosine, manganese saok

SM: GMP

9v29

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Cryo- EM structure of small subunit (body) of 75S ribosome with A/P- & P/E- tRNAs from Entamoeba histolytica bound to antibiotic paromomycin

SM: PAR

9v4u

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Crystal structure of Guanine-II riboswitch in complex with 7,8-dihydroneopterin

SM: NPR

9v4v

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Crystal structure of Guanine-II riboswitch in complex with isoxanthopterin

SM: 7PD

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

9vmz

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Crystal structure of Broccoli aptamer in with BI

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

9yd3

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RNA primer non-enzymatic extension product with RNA substrate

SM: EQ4

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Experimental method

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

Alpharetrovirus

Anabaena

Arabidopsis

Azoarcus

Bacillus

Betacoronavirus

Bifidobacterium

Bos

Caldanaerobacter

Candida

Candidatus Korobacter

Candidatus Pelagibacter

Chlamydomonas

Clostridium

Coxiella

Cutibacterium

Deinococcus

Didymium

Entamoeba

Enterovirus

Escherichia

Faecalibacterium

Francisella

Fusobacterium

Geobacter

Gloeobacter

Haloarcula

Hepacivirus

Homo

Ideonella

Lacticaseibacillus

Lactococcus

Leishmania

Lentivirus

Listeria

Mesoplasma

Mesorhizobium

Mus

Mycobacterium

Mycolicibacterium

Mycoplasmoides

Nicotiana

Oceanobacillus

Oryctolagus

Paenibacillus

Porphyromonas

Pseudomonas

Pylaiella

Pyrobaculum

Ralstonia

Roseobacter

Ruminococcus

Saccharolobus

Saccharomyces

Schaalia

Staphylococcus

Streptococcus

Streptomyces

Sulfobacillus

Sus

Syntrophothermus

Tequatrovirus

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

Select cutoff values for the SiteScore, ligandability score calcultated by Schrödinger tool. Below 0.8 the pocket is considered non-drug binding site, between 0.8 and 1.0 a potential drug binding site, and above 1.0 a promising binding site [TODO add ref]

Current selection range: to

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

Select cutoff values for the exposure, a score calculated by Schrödinger tool which indicates the degree of exposure to the solvent of the pocket (AU)

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Enclosure

Select cutoff values for the enclosure, a score calculated by Schrödinger tool which indicates the degree of buriedness of the pocket (AU)

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Hydrophobicity

Select cutoff values for the hydrophobicity, a score calculated by Schrödinger tool which indicates the degree of hydrophobicity of the pocket (AU)

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Hydrophilicity

Select cutoff values for the hydrophilicity, a score calculated by Schrödinger tool which indicates the degree of hydrophilicity of the pocket (AU)

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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 environment detailed

DNA

ion

other

protein

RNA-only

RNA family global

RNA/DNA_hybrid

TAR_rna

aptamer_rna

mRNA

multiple

rRNA

riboswitch

ribozyme

snRNA

sre_rna

synthetic construct

tRNA

telomerase_RNA

unknown

RNA family chains

aptamer_rna

mRNA

riboswitch

ribozyme

RNA/DNA_hybrid

rRNA

snRNA

sre_rna

synthetic construct

TAR_rna

telomerase_RNA

tRNA

unknown

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