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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)

1918 RNA-SM complexes found

RNA-SM complexes per page

60 120 180

filters used: With equivalence class

Structure of complex 9nap

9nap

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RNA scaffold attached to Mango in the presence of TO1-biotin

SM: EKJ

Structure of complex 9nbc

9nbc

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RNA scaffold attached to 8-oxoguanine riboswitch aptamer

SM: OXG

Structure of complex 9ndd

9ndd

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RNA scaffold attached to 8-oxoguanine riboswitch aptamer, combined core plus aptamer

SM: OXG OXG OXG OXG

Structure of complex 9ndv

9ndv

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Scaffold attached to quinine-I aptamer (Tonic) local refinement of aptamer

SM: QI9

Structure of complex 9ndx

9ndx

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Scaffold attached to quinine-I aptamer (Tonic) refinement of aptamer and core

Structure of complex 9nl2

9nl2

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Structure of R2 retrotransposon protein from Platysternon megacephalum initiating target-primed reverse transcription

SM: TTP

Structure of complex 9nl3

9nl3

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Structure of R2 retrotransposon protein from Taeniopygia guttata initiating target-primed reverse transcription

SM: TTP

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 9ol2

9ol2

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RNA-imidazolium-bridged dinucleotide intermediate complex

Structure of complex 9ol3

9ol3

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DNA-imidazolium-bridged dinucleotide intermediate complex

SM: A1CGJ A1CGJ

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 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 9pde

9pde

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Three-dimensional structure of kinase inhibitor Palbociclib-HIV TAR complex

SM: LQQ

Structure of complex 9pdf

9pdf

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Three-dimensional structure of kinase inhibitor Palbociclib-HIV TAR complex

SM: LQQ

Structure of complex 9pdg

9pdg

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Three-dimensional structure of kinase inhibitor Palbociclib-HIV TAR complex

SM: LQQ

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 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

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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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Current selection range: to

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

Deposition date

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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

Alpharetrovirus

Anabaena

Arabidopsis

Archaeoglobus

Azoarcus

Bacillus

Bacteroides

Bandavirus

Betacoronavirus

Betainfluenzavirus

Bifidobacterium

Bombyx

Bos

Brassica

Caenorhabditis

Caldanaerobacter

Candida

Candidatus Korobacter

Candidatus Pelagibacter

Candidozyma

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

Tetrahymena

Thermoanaerobacter

Thermochaetoides

Thermotoga

Thermovirga

Thermus

Thogotovirus

Tilapinevirus

Tribolium

Trichoplusia

Triticum

Trypanosoma

Tymovirus

Varicellovirus

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

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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

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

Enclosure

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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/DNA

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

aptamer_rna

mRNA

riboswitch

ribozyme

RNA/DNA_hybrid

rRNA

snRNA

sre_rna

synthetic construct

TAR_rna

telomerase_RNA

tRNA

unknown

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