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Harnessing RIBOnucleic acid - Small molecules Structures

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RNA-SM complexes
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RNA-SM complexes

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System Properties

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

Ligand Properties

Molecular weight (Da) Number of atoms 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)

964 RNA-SM complexes found

RNA-SM complexes per page

60 120 180

filters used: RNA family global: rRNA

Structure of complex 9i88

9i88

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Structure of the wild-type Staphylococcus aureus 70S ribosome complexed with clincelin

Structure of complex 9i89

9i89

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Structure of the A2058-dimethylated Staphylococcus aureus 70S ribosome complexed with clincelin

Structure of complex 9k0z

9k0z

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EF-G2 bound 70S ribosome complex of M. smegmatis

SM: PHE

Structure of complex 9mkk

9mkk

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Structure of arbekacin bound Escherichia coli 70S ribosome

Structure of complex 9mnc

9mnc

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Human 80S ribosome bound to small molecule SW393071

Structure of complex 9muj

9muj

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RlmR 23S rRNA methyltransferase from Thermus thermophilus in complex with methylated rRNA (Um2552) and S-adenosyl-L-homocysteine (SAH)

SM: SAH

Structure of complex 9n2b

9n2b

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Impacts of ribosomal RNA sequence variation on gene expression and phenotype: Cryo-EM structure of the rrsB ribosome (BBB-70S)

Structure of complex 9n2c

9n2c

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Impacts of ribosomal RNA sequence variation on gene expression and phenotype: Cryo-EM structure of the rrsH ribosome (HBB-70S)

Structure of complex 9n5t

9n5t

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Mycobacterium smegmatis 70S ribosome with small molecule drug MK-7762

Structure of complex 9o2x

9o2x

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Structure of WT E.coli ribosome 70S subunit with complexed with mRNA, P-site fMet-NH-tRNAfMet and A-site (S)-betahydroxyBocK charged NH-tRNAPyl

Structure of complex 9o2y

9o2y

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Structure of WT E.coli ribosome 70S subunit with complexed with mRNA, P-site fMet-NH-tRNAfMet and A-site (R) beta-2-hydroxy-BocLysine acid charged NH-tRNAPyl

Structure of complex 9o3h

9o3h

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Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with macrolide erythromycin, mRNA, aminoacylated A-site Lys-tRNAlys, P-site fMRC-peptidyl-tRNAmet, and deacylated E-site tRNAlys at 2.65A resolution

Structure of complex 9o3i

9o3i

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Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with ketolide telithromycin, mRNA, aminoacylated A-site Lys-tRNAlys, P-site fMRC-peptidyl-tRNAmet, and deacylated E-site tRNAlys at 2.80A resolution

Structure of complex 9o3k

9o3k

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Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with macrolide erythromycin, mRNA, aminoacylated A-site Lys-tRNAlys, P-site fMAC-peptidyl-tRNAmet, and deacylated E-site tRNAlys at 2.70A resolution

Structure of complex 9o3l

9o3l

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Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with macrolide erythromycin, mRNA, deacylated A-site tRNAphe, P-site fMRC-peptidyl-tRNAmet, and deacylated E-site tRNAphe at 2.75A resolution

Structure of complex 9o3w

9o3w

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Human 80S ribosome bound to IDB-001 stalled on MYC nascent chain

Structure of complex 9o3y

9o3y

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Human 80S ribosome bound to IDB-002 stalled on FPAK-containing nascent chain

Structure of complex 9olf

9olf

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Membrane-associated human mitoribosome in complex with TACO1

SM: NAD SPM SPM

Structure of complex 9p6z

9p6z

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In situ human P-Z state 80S ribosome

SM: SPM SPM SPM SPM SPM SPM SPM

Structure of complex 9p72

9p72

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In situ human P-E state 80S ribosome

SM: SPM SPM SPM SPM SPM SPM SPM

Structure of complex 9p73

9p73

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In situ human eEF2-A/P-P/E state 80S ribosome

SM: SPM SPM SPM SPM SPM SPM SPM

Structure of complex 9p76

9p76

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In situ human eEF1A-A/T-P state 80S ribosome

SM: SPM SPM SPM SPM SPM SPM SPM

Structure of complex 9p78

9p78

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In situ human Hibernating rotate 3 with E-site tRNA state 80S ribosome

SM: SPM SPM SPM SPM SPM SPM SPM

Structure of complex 9p79

9p79

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In situ human Hibernating rotate3 with Z site tRNA state 80S ribosome

SM: SPM SPM SPM SPM SPM SPM SPM

Structure of complex 9p7a

9p7a

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In situ human hibernating class2 80S ribosome

SM: SPM SPM SPM SPM SPM SPM SPM

Structure of complex 9p7c

9p7c

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In situ human Hibernating class3 80S ribosome

SM: SPM SPM SPM SPM SPM SPM SPM

Structure of complex 9p7d

9p7d

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In situ human Hibernating class4 80S ribosome

SM: SPM SPM SPM SPM SPM SPM SPM

Structure of complex 9p7e

9p7e

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In situ human Hibernating class5 80S ribosome

SM: SPM SPM SPM SPM SPM SPM SPM

Structure of complex 9p7f

9p7f

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In situ HHT and CHX treated A-P state 80S ribosome

SM: HMT SPM SPM SPM SPM SPM SPM SPM

Structure of complex 9p7g

9p7g

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In situ HHT and CHX treated A-P-Z state 80S ribosome

SM: HMT SPM SPM SPM SPM SPM SPM SPM

Structure of complex 9p7h

9p7h

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In situ HHT and CHX treated human eEF1A-A/T-P state 80S ribosome

SM: 3HE HMT SPM SPM SPM SPM SPM SPM SPM

Structure of complex 9p7i

9p7i

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In situ HHT and CHX treated human eEF1A-A/T-P-Z state 80S ribosome

SM: 3HE HMT SPM SPM SPM SPM SPM SPM SPM

Structure of complex 9p7j

9p7j

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In situ HHT and CHX treated human P state 80S ribosome

SM: 3HE HMT SPM SPM SPM SPM SPM SPM SPM

Structure of complex 9p7k

9p7k

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In situ human post eEF1A-A/T-P-E state 80S ribosome

SM: SPM SPM SPM SPM SPM SPM SPM

Structure of complex 9p7l

9p7l

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In situ human Post-eEF1A-AT-P state 80S ribosome

SM: SPM SPM SPM SPM SPM SPM SPM

Structure of complex 9p7n

9p7n

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In situ human Post-eEF1A-A/T-P-Z state 80S ribosome

SM: SPM SPM SPM SPM SPM SPM SPM

Structure of complex 9p7o

9p7o

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In situ human AT-P-Z state ribosome

SM: SPM SPM SPM SPM SPM SPM SPM

Structure of complex 9p7w

9p7w

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In situ human A-P state 80S ribosome

SM: SPM SPM SPM SPM SPM SPM SPM

Structure of complex 9p7x

9p7x

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In situ human A-P-Z state 80S ribosome

SM: SPM SPM SPM SPM SPM SPM SPM

Structure of complex 9p7y

9p7y

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In situ human A-P-E state 80S ribosome

SM: SPM SPM SPM SPM SPM SPM SPM

Structure of complex 9p8b

9p8b

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In situ human eEF1A-A/T-P-E state 80S ribosome

SM: SPM SPM SPM SPM SPM SPM SPM

Structure of complex 9p8c

9p8c

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In situ human Hibernating class1 (rotate3) without E tRNA state 80S ribosome

SM: SPM SPM SPM SPM SPM SPM SPM

Structure of complex 9p8h

9p8h

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In situ human A/P-P/E state 80S ribosome

SM: SPM SPM SPM SPM SPM SPM SPM

Structure of complex 9p8i

9p8i

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In situ HHT and CHX treated human P-Z state 80S ribosome

SM: 3HE HMT SPM SPM SPM SPM SPM SPM SPM

Structure of complex 9p9h

9p9h

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In situ human unrotated hibernating with CCDC124 state 80S ribosome

SM: SPM SPM SPM SPM SPM SPM SPM

Structure of complex 9p9i

9p9i

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In situ human unrotated hibernating without CCDC124 state 80S ribosome

SM: SPM SPM SPM SPM SPM SPM SPM

Structure of complex 9p9j

9p9j

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In situ human 60S ribosome

SM: SPM SPM SPM SPM SPM SPM SPM

Structure of complex 9p9k

9p9k

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In situ human 60S ribosome with EIF6

SM: SPM SPM SPM SPM SPM SPM SPM

Structure of complex 9pa7

9pa7

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In situ human 80S consensus ribosome with EBP1

SM: SPM SPM SPM SPM SPM SPM SPM SPM

Structure of complex 9pbe

9pbe

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In situ human 80S ribosome (composite map)

SM: SPM SPM SPM SPM SPM SPM SPM SPM

Structure of complex 9pg8

9pg8

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

SM: NAD SPM SPM SPM

Structure of complex 9pgf

9pgf

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In situ structure of the human mitoribosome in the P state

SM: NAD SPM SPM SPM

Structure of complex 9pgi

9pgi

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In situ structure of the human mitoribosome in the A-P-E state with TACO1

SM: NAD SPM SPM

Structure of complex 9pgl

9pgl

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In situ structure of the human mitoribosome in the A-P state with TACO1

SM: NAD SPM SPM

Structure of complex 9pgm

9pgm

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

SM: NAD SPM SPM

Structure of complex 9pih

9pih

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E. coli 70S ribosome bound to Doxycycline

SM: DXT DXT DXT DXT DXT DXT

Structure of complex 9pii

9pii

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E. coli 70S ribosome bound to Sarecycline

Structure of complex 9pij

9pij

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E. coli 70S ribosome bound to Minocycline

Structure of complex 9pj7

9pj7

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C. acnes 70S ribosome bound to Doxycycline

SM: DXT DXT DXT DXT DXT DXT DXT

Structure of complex 9pj8

9pj8

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C. acnes 70S ribosome bound to Sarecycline

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Experimental method

Experimental resolution

Select cutoff values for experimental resolution (Å)

Current selection range: to

Filter entries " Experimental resolution " between the two values. Global DB range: 0.6 – 11.2

Molecular weight (compound)

Select cutoff values for molecular weight of the compound (Da)

Current selection range: to

Filter entries " Molecular weight (compound) " between the two values. Global DB range: 150 – 1000

Deposition date

Select cutoff values for the deposition date (years) of the PDB entries

Current selection range: to

Filter entries " Deposition date " between the two values. Global DB range: 1986 – 2027

Molecular composition of the system

RNA

RNA/DNA/Protein

RNA/Protein

Source organism

Acinetobacter

Arabidopsis

Bacillus

Betacoronavirus

Bos

Brassica

Caenorhabditis

Candida

Candidozyma

Chlamydomonas

Coxiella

Cutibacterium

Deinococcus

Entamoeba

Enterococcus

Enterovirus

Escherichia

Francisella

Giardia

Haloarcula

Hepacivirus

Homo

Kluyveromyces

Leishmania

Listeria

Mus

Mycobacterium

Mycolicibacterium

Mycoplasmoides

Neurospora

Nicotiana

Oryctolagus

Plasmodium

Porphyromonas

Pyrobaculum

Saccharolobus

Saccharomyces

Solanum

Staphylococcus

Streptomyces

Sulfolobus

Sus

Tequatrovirus

Thermochaetoides

Thermus

Triticum

Trypanosoma

Vibrio

Molecular weight (complex)

Select cutoff values for molecular weight of the system complex (kDa)

Current selection range: to

Filter entries " Molecular weight (complex) " between the two values. Global DB range: 0 – 13090

Number of atoms

Select cutoff values for the number of atoms of the compounds

Current selection range: to

Filter entries " Number of atoms " between the two values. Global DB range: 5 – 70

Number of interacting chains

Select cutoff values for the number of interacting RNA chains in the pockets

Current selection range: to

Filter entries " Number of interacting chains " between the two values. Global DB range: 1 – 4

Pocket size

Select cutoff values for the number of heavy RNA atoms in the pocket

Current selection range: to

Filter entries " Pocket size " between the two values. Global DB range: 15.9 – 394.0

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 (Halgren 2009, SiteMap)

Current selection range: to

Filter entries " SiteScore " between the two values. Global DB range: 0.3 – 1.3

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 (Halgren 2009, SiteMap)

Current selection range: to

Filter entries " Dscore " between the two values. Global DB range: -0.1 – 1.4

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)

Current selection range: to

Filter entries " Exposure " between the two values. Global DB range: 0.1 – 1.0

Enclosure

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

Current selection range: to

Filter entries " Enclosure " between the two values. Global DB range: 0.3 – 1.0

Hydrophobicity

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

Current selection range: to

Filter entries " Hydrophobicity " between the two values. Global DB range: 0.0 – 3.1

Hydrophilicity

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

Current selection range: to

Filter entries " Hydrophilicity " between the two values. Global DB range: 0.2 – 2.8

Donor/Acceptor

Select cutoff values for Donor/Acceptor character of the pocket calculated by Schrödinger tool

Current selection range: to

Filter entries " Donor/Acceptor " between the two values. Global DB range: 0.0 – 5.0

Volume

Select cutoff values for volume of the pocket calculated by Schrödinger tool (Å³)

Current selection range: to

Filter entries " Volume " between the two values. Global DB range: 21.2 – 1528.8

RNA environment global

RNA

RNA/DNA/Protein

RNA/Other

RNA/Protein

RNA environment detailed

DNA

RNA-only

ion

other

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

RNA family chains

mRNA

rRNA

tRNA

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