HARIBOSS

Harnessing RIBOnucleic acid - Small molecules Structures

Compounds
RNA-SM complexes
About

You are here

Complexes

× Close

System Properties

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

Ligand Properties

Molecular weight Number of atoms Number of PDB entries 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)

7 Complexes found

Complexes per page

60 120 180

filters used: RNA family global: sre_rna

Select this complex

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

SM: NMY

Select this complex

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

Select this complex

Cryo-EM structure of Tetrahymena ribozyme conformation 1 undergoing the first-step self-splicing

SM: GTP

Select this complex

Cryo-EM structure of Tetrahymena ribozyme conformation 2 undergoing the first-step self-splicing

SM: GTP

Select this complex

Cryo-EM structure of Tetrahymena ribozyme conformation 3 undergoing the first-step self-splicing

SM: GTP

Select this complex

Cryo-EM structure of Tetrahymena ribozyme conformation 4 undergoing the first-step self-splicing

SM: GTP

Select this complex

Structure of Oceanobacillus iheyensis group II intron post first step of splicing in the presence of K+, Mg2+ and intronistat B

SM: EPE SPM

1 of 1
Go to page

Experimental method

Experimental resolution

Select cutoff values for experimental resolution (Å)

Current selection range: to

Molecular Weight

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

Current selection range: to

Deposition date

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

Current selection range: to

Molecular composition of the system

RNA

Source organism

Homo

Oceanobacillus

Tetrahymena

Molecular weight

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

Current selection range: to

Number of atoms

Select cutoff values for the number of atoms of the compounds

Current selection range: to

Number of PDB entries

Select cutoff values for the number of PDB entries where the compounds have been resolved

Current selection range: to

Number of interacting chains

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

Current selection range: to

Pocket size

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

Current selection range: to

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 [TODO add ref]

Current selection range: to

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 [TODO add ref]

Current selection range: to

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

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

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

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

Donor/Acceptor

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

Current selection range: to

Volume

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

Current selection range: to

RNA environment global

RNA

RNA/DNA

RNA/DNA/Protein

RNA/Other

RNA/Protein

RNA environment detailed

DNA

ion

other

protein

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

aptamer_rna

mRNA

riboswitch

ribozyme

RNA/DNA_hybrid

rRNA

snRNA

sre_rna

synthetic construct

TAR_rna

telomerase_RNA

tRNA

unknown

25-28 Rue du Dr ROUX,
75015 Paris

01 45 68 80 00

About
Contact
Credits
Policies

HARIBOSS

Complexes

1ei2

Select this complex

6hmo

Select this complex

7yc8

Select this complex

7ycg

Select this complex

7ych

Select this complex

7yci

Select this complex

8oly

Select this complex