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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)

93 RNA-SM complexes found

RNA-SM complexes per page

60 120 180

filters used: RNA family global: multiple

Structure of complex 8ud7

8ud7

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Crystal structure of the A2058-N6-dimethylated Thermus thermophilus 70S ribosome in complex with cresomycin, mRNA, deacylated A-site tRNAphe, aminoacylated P-site fMet-tRNAmet, and deacylated E-site tRNAphe at 2.70A resolution

Structure of complex 8ud8

8ud8

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Crystal structure of the A2503-C2,C8-dimethylated Thermus thermophilus 70S ribosome in complex with cresomycin, mRNA, deacylated A-site tRNAphe, aminoacylated P-site fMet-tRNAmet, and deacylated E-site tRNAphe at 2.70A resolution

SM: WC9

Structure of complex 8vft

8vft

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Translating 80S rabbit ribosome stalled by emetine with eEF2

SM: 34G

Structure of complex 8xsx

8xsx

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Cryo-EM structure of the human 80S ribosome with Tigecycline, E-tRNA, SERBP1 and eEF2

SM: T1C T1C T1C T1C T1C T1C T1C

Structure of complex 8xsy

8xsy

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Cryo-EM structure of the human 80S ribosome with Tigecycline, e-tRNA and CCDC124 (40S head Swivelled)

SM: T1C T1C T1C T1C T1C T1C T1C T1C

Structure of complex 9d0g

9d0g

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Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with O-cresomycin, mRNA, deacylated A-site tRNAphe, aminoacylated P-site fMet-tRNAmet, and deacylated E-site tRNAphe at 2.50A resolution

SM: A1A1F A1A1F

Structure of complex 9d0h

9d0h

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Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with C-cresomycin, mRNA, deacylated A-site tRNAphe, aminoacylated P-site fMet-tRNAmet, and deacylated E-site tRNAphe at 2.50A resolution

SM: A1A1J A1A1J

Structure of complex 9d0i

9d0i

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Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with Se-cresomycin, mRNA, deacylated A-site tRNAphe, aminoacylated P-site fMet-tRNAmet, and deacylated E-site tRNAphe at 2.45A resolution

SM: A1A1K A1A1K

Structure of complex 9d0j

9d0j

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Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with BT-33, mRNA, deacylated A-site tRNAphe, aminoacylated P-site fMet-tRNAmet, and deacylated E-site tRNAphe at 2.50A resolution

SM: A1A1L A1A1L

Structure of complex 9fco

9fco

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Structure of E. coli 30S-IF1-IF3-mRNA-Kasugamycin complex

SM: KSG

Structure of complex 9g30

9g30

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The structure of the Candida albicans ribosome with tRNA-fMet, mRNA, and compounds (GEN and MFQ) shows strong density for the A site tRNA

SM: GET GET GET GET GET GET GET GET GET GET GET GET GET GET GET GET GET SPK

Structure of complex 9h6i

9h6i

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Structure of the Arabidopsis thaliana 80S ribosome in complex with P- and E-site tRNAs, mRNA, and thermospermine

SM: EPE TER TER TER TER TER TER TER TER TER TER TER TER TER TER TER TER TER TER TER TER TER TER TER TER TER TER TER

Structure of complex 9g06

9g06

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Structure of 30S-IF1-IF3-mRNA-fMet-tRNA-GE81112A complex

Structure of complex 9gr1

9gr1

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E. coli 70S-TEC complex in delivery state

SM: PHE

Structure of complex 9h9h

9h9h

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Complex 1 30S-IF1-IF2-IF3-GE81112

Structure of complex 9hes

9hes

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Structure of the Arabidopsis thaliana 80S ribosome OVAC mutant in complex with P- and E-site tRNAs, mRNA, and thermospermine

SM: EPE TER TER TER TER TER TER TER TER TER TER TER TER TER TER TER TER TER TER TER TER TER TER TER TER TER TER TER

Structure of complex 9i14

9i14

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CRYO-EM STRUCTURE OF HCT15 POLYSOMES IN HYBRID-PRE STATE

SM: HYG

Structure of complex 9mkk

9mkk

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Structure of arbekacin bound Escherichia coli 70S ribosome

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 9qsj

9qsj

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

Structure of complex 9ru7

9ru7

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

SM: HYG

Structure of complex 9ru8

9ru8

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

SM: HYG

Structure of complex 9ru9

9ru9

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

Structure of complex 9spf

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

Structure of complex 9spi

9spi

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

SM: HYG

Structure of complex 9sro

9sro

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

Structure of complex 9vxm

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 NMY NMY NMY NMY NMY NMY NMY SPM

Structure of complex 9vxn

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 NMY NMY NMY NMY NMY NMY NMY NMY NMY NMY NMY NMY NMY NMY NMY NMY

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Experimental method

Experimental resolution

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Current selection range: to

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

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/Protein

Source organism

Arabidopsis

Candida

Cutibacterium

Escherichia

Giardia

Homo

Leishmania

Mycolicibacterium

Oryctolagus

Saccharomyces

Tequatrovirus

Tetrahymena

Thermus

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/Other

RNA/Protein

RNA environment detailed

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

ribozyme

rRNA

sre_rna

tRNA

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