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)

812 Complexes found

Complexes per page

60 120 180

filters used: RNA environment global: RNA/Protein

9qqq

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Cryo-EM structure of SKM-70S ribosomal stalled complex in the major state (vacant A-site, canon)

9qsj

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Cryo-EM structure of SKM-70S ribosomal stalled complex in the A-tRNA positioned (Body open) state.

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)

9rpf

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Assembly intermediate of human mitochondrial ribosome small subunit bound to METTL15 and mS37 (State M4)

SM: NAD

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)

9ru6

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Human mitoribosome bound to TACO1 (Translational activator of COX1), mRNA, A/A-, P/P- and (partial) E/E-tRNAs

SM: NAD

9sdf

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Structure at 1.9 A resolution of Thermus thermophilus tyrosyl-tRNA synthetase bound to wild-type modified tRNA(Tyr), tyrosine and AMP

SM: 1PE

9sfq

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Structure at 1.9 A resolution of Thermus thermophilus tyrosyl-tRNA synthetase bound to wild-type tRNATyr(GUC).

SM: 1PE

9sro

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Cryo-EM structure of SKM-70S ribosomal stalled complex in the rotated state with hybrid tRNAs

9t6h

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

9tmi

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E. coli 70S ribosome with A- and P-site tRNA

SM: SCM

9tnl

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E. coli 70S ribosome with A/P- and P/E-site tRNA

SM: SCM

9tqa

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E. coli 70S ribosome, trapped conformational ground state of SSU-h44 apical loop, with A- and P-site tRNA

SM: SCM

9uht

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SARS-CoV-2 E-RTC in complex with RNA-nsp9 and GMPPNP

SM: GNP

9uwh

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human mitoribosome trapped by retapamulin

9v26

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

SM: PAR

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

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

Experimental resolution

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Molecular Weight

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Deposition date

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Molecular composition of the system

RNA/DNA/Protein

RNA/Protein

Source organism

Acinetobacter

Alphainfluenzavirus

Arabidopsis

Archaeoglobus

Bacillus

Bandavirus

Betacoronavirus

Betainfluenzavirus

Bos

Brassica

Caenorhabditis

Candida

Cypovirus

Deinococcus

Entamoeba

Enterococcus

Escherichia

Francisella

Giardia

Halalkalibacterium (ex Joshi et al. 2022)

Haloarcula

Henipavirus

Homo

Kluyveromyces

Leishmania

Listeria

Mammarenavirus

Mus

Mycobacterium

Mycolicibacterium

Mycoplasmoides

Neurospora

Nicotiana

Orthobunyavirus

Orthoflavivirus

Orthonairovirus

Orthopneumovirus

Orthoreovirus

Oryctolagus

Plasmodium

Pyrobaculum

Rauchvirus

Rotavirus

Saccharolobus

Saccharomyces

Segatella

Solanum

Staphylococcus

Streptococcus

Streptomyces

Sulfolobus

Sus

Tequatrovirus

Thermochaetoides

Thermotoga

Thermus

Thogotovirus

Tilapinevirus

Triticum

Trypanosoma

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

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]

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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

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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