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Harnessing RIBOnucleic acid - Small molecules Structures

Compounds
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)

1215 RNA-SM complexes found

RNA-SM complexes per page

60 120 180

filters used: Molecule type: RNA/Protein

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 9olf

9olf

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Membrane-associated human mitoribosome in complex with TACO1

SM: NAD SPM SPM

Structure of complex 9p6p

9p6p

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Crystal Structure of the SARS-CoV-2 2'-O-Methyltransferase with (m7GpppA)pUpU (Cap-0) and S-Adenosyl-L-homocysteine (SAH).

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 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 9pfr

9pfr

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Cryo-EM structure of the respiratory syncytial virus polymerase (L:P) in NTP-bound elongation state

SM: ZAN

Structure of complex 9pfs

9pfs

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Cryo-EM structure of the respiratory syncytial virus polymerase (L:P) in pre-reaction elongation state

SM: ZAN

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 9q6s

9q6s

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Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with pleuromutilin-30 triazole derivative and protein Y at 2.90A resolution

SM: A1CQ8 A1CQ8 ARG ARG

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

Structure of complex 9pj9

9pj9

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C. acnes 70S ribosome bound to Minocycline

SM: MIY MIY MIY

Structure of complex 9pkb

9pkb

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

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

Structure of complex 9pkd

9pkd

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In situ CHX and HHT treated 80S consensus ribosome

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

Structure of complex 9pkg

9pkg

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In situ human P state 80S ribosome

SM: SPM SPM SPM SPM SPM SPM SPM

Structure of complex 9prd

9prd

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

SM: NAD SPM SPM

Structure of complex 9prq

9prq

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

SM: NAD SPM SPM

Structure of complex 9prx

9prx

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

SM: NAD SPM SPM

Structure of complex 9ps0

9ps0

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

SM: NAD SPM SPM

Structure of complex 9ps7

9ps7

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

SM: NAD SPM SPM

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Experimental method

Experimental resolution

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

Molecular weight (compound)

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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

RNA/DNA/Protein

RNA/Protein

Source organism

Acidobacterium

Acinetobacter

Alphainfluenzavirus

Arabidopsis

Archaeoglobus

Bacillus

Bacteroides

Bandavirus

Betacoronavirus

Betainfluenzavirus

Bifidobacterium

Bos

Brassica

Caenorhabditis

Caldanaerobacter

Candida

Candidozyma

Chlamydomonas

Coxiella

Cutibacterium

Cypovirus

Deinococcus

Desulfonema

Entamoeba

Enterococcus

Escherichia

Francisella

Giardia

Halalkalibacterium (ex Joshi et al. 2022)

Haloarcula

Henipavirus

Homo

Leishmania

Listeria

Mammarenavirus

Mus

Mycobacterium

Mycolicibacterium

Mycoplasmoides

Neurospora

Nicotiana

Orthobunyavirus

Orthoflavivirus

Orthonairovirus

Orthopneumovirus

Orthoreovirus

Oryctolagus

Plasmodium

Porphyromonas

Pyrobaculum

Rauchvirus

Rotavirus

Ruminococcus

Saccharolobus

Saccharomyces

Segatella

Solanum

Staphylococcus

Streptococcus

Streptomyces

Sulfolobus

Sus

Tequatrovirus

Thermochaetoides

Thermotoga

Thermus

Thogotovirus

Tilapinevirus

Triticum

Trypanosoma

Vesiculovirus

Vibrio

Molecular weight (complex)

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

Number of atoms

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

Number of interacting chains

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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

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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)

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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)

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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)

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

Hydrophobicity

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

Hydrophilicity

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

Donor/Acceptor

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

Volume

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

RNA environment global

RNA

RNA/Other

RNA/Protein

RNA environment detailed

RNA-only

ion

other

protein

RNA family global

TAR_rna

aptamer_rna

mRNA

multiple

rRNA

riboswitch

ribozyme

snRNA

synthetic construct

tRNA

unknown

RNA family chains

aptamer_rna

mRNA

riboswitch

ribozyme

rRNA

snRNA

synthetic construct

TAR_rna

tRNA

unknown

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