HARIBOSS

Harnessing RIBOnucleic acid - Small molecules Structures

Compounds
RNA-SM complexes
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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)

20 Complexes found

Complexes per page

60 120 180

filters used: Molecule type: RNA/DNA

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1.66 A STRUCTURE OF A-DUPLEX WITH BULGED ADENOSINE, SPERMINE FORM

SM: SPM

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Crystal Structure of the B-DNA Hexamer (CgATCG).Daunomycin Complex Containing a Ribose at the Intercalation Site

SM: DM1

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CRYSTAL STRUCTURE OF AN OKAZAKI FRAGMENT AT 2 ANGSTROMS RESOLUTION

SM: SPM

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CRYSTAL STRUCTURES OF THE B-FORM DNA-RNA CHIMER (5'-D(*IP*)-R(*CP*)-D(*IP*CP*IP*CP*IP*C)-3') COMPLEXED WITH DISTAMYCIN

SM: DMY

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CRYSTAL STRUCTURES OF THE B-FORM DNA-RNA CHIMER (5'-D(*IP*)-R(*CP*)-D(*IP*)-R(*CP*)-D(*IP*CP*IP*C)-3') COMPLEXED WITH DISTAMYCIN

SM: DMY

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CRYSTAL STRUCTURES OF AN A-FORM DUPLEX WITH SINGLE-ADENOSINE BULGES AND A CONFORMATIONAL BASIS FOR SITE SPECIFIC RNA SELF-CLEAVAGE

SM: SPM

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Pre-cleavage state of the Thermoanaerobacter tengcongensis glmS ribozyme bound to glucose-6-phosphate

SM: G6P

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T. tengcongensis glmS ribozyme bound to glucose-6-phosphate

SM: G6P

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T. tengcongensis glmS ribozyme bound to glucosamine-6-phosphate

SM: GLP

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Crystal structure of HIV-1 subtype F DIS extended duplex RNA bound to ribostamycin

SM: RIO

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Crystal structure of HIV-1 subtype F DIS extended duplex RNA bound to lividomycin

SM: LIV

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Crystal Structure of HIV-1 subtype F DIS extended duplex RNA bound to neomycin

SM: NMY

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DNA modification at 3' end of RNA primer complex with guanosine dinucleotide ligand G(5')ppp(5')G

SM: GP3

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Crystal structure of DNA/RNA duplex obtained using the counter diffusion method on Earth (K form)

SM: SPM

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Crystal structure of DNA/RNA duplex obtained using the counter diffusion method on Earth (Na form)

SM: SPM

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Crystal structure of DNA/RNA duplex obtained using the counter diffusion method in space (Na form)

SM: SPM

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INTERACTION BETWEEN A FLUOROQUINOLONE DERIVATIVE AND RNAS WITH A SINGLE BULGE

SM: 53D

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INTERACTION BETWEEN A FLUOROQUINOLONE DERIVATIVE AND RNAS WITH A SINGLE BULGE

SM: 53D

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Crystal structure of the DNA/RNA hybrid with Tica

SM: A1ETT

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RNA primer non-enzymatic extension product with DNA substrate

SM: A1CWA

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Experimental method

Experimental resolution

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Molecular Weight

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Deposition date

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Molecular composition of the system

RNA/DNA

RNA

RNA/DNA/Protein

RNA/Protein

Source organism

Caldanaerobacter

Mus

Molecular weight

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Number of atoms

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Number of PDB entries

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

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Number of interacting chains

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

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Pocket size

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

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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)

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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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Hydrophobicity

Select cutoff values for the hydrophobicity, a score calculated by Schrödinger tool which indicates the degree of hydrophobicity of the pocket (AU)

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Hydrophilicity

Select cutoff values for the hydrophilicity, a score calculated by Schrödinger tool which indicates the degree of hydrophilicity of the pocket (AU)

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Donor/Acceptor

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

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Volume

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

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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

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