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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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Combine filters to refine your query. Each filter opens a dialog showing the values available in the data.

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)

2 RNA-SM complexes found

RNA-SM complexes per page

60 120 180

filters used: RNA family global: sre_rna

Structure of complex 1ei2

1ei2

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STRUCTURAL BASIS FOR RECOGNITION OF THE RNA MAJOR GROOVE IN THE TAU EXON 10 SPLICING REGULATORY ELEMENT BY AMINOGLYCOSIDE ANTIBIOTICS

SM: NMY

Structure of complex 6hmo

6hmo

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Solution structure of the RNA duplex formed by the 5'-end of U1snRNA and the 5'-splice site of SMN2 exon7 in complex with the SMN-C5 splicing modifier

SM: GDZ

1 of 1
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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

Source organism

Homo

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 environment detailed

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

sre_rna

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