HARIBOSS

Harnessing RIBOnucleic acid - Small molecules Structures

Compounds
RNA-SM complexes
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Complexes

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)

207 Complexes found

Complexes per page

60 120 180

filters used: RNA family global: synthetic construct

8xpo

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Cryo-EM structure of Lassa virus RdRP elongation complex with the NTP form of compound HNC-1664 bound in the active site

8yno

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RNA duplex containing Formamide

SM: SPM

9bdd

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Cryo-EM Structure of Non-Cognate Substrate Bound in the Entry Site (ES) of Human Mitochondrial Transcription Elongation Complex

SM: APC

9blf

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SARS-CoV-2 core polymerase complex inhibited by araCTP

SM: HF4

9j6p

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pre-mir-125a internal loop in complex with G-clamp

9ja1

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The RNA polymerase II elongation complex from Saccharomyces cerevisiae

SM: ATP

9ljr

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Structural insights into the polymerase catalyzed FAD-capping of hepatitis C viral RNA

9ljs

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Structural insights into the polymerase catalyzed FAD-capping of hepatitis C viral RNA

9ljt

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Structural insights into the polymerase catalyzed FAD-capping of hepatitis C viral RNA

9lju

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Structural insights into the polymerase catalyzed FAD-capping of hepatitis C viral RNA

9ljv

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Structural insights into the polymerase catalyzed FAD-capping of hepatitis C viral RNA

9ljw

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Structural insights into the polymerase catalyzed FAD-capping of hepatitis C viral RNA

SM: GDP

9mn6

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Structure of the human mitochondrial late-stage transcription initiation complex, IC8

SM: ATP

9mn7

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Structure of the human mitochondrial late-stage transcription initiation complex, IC8

SM: ATP

9mn8

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Structure of the human mitochondrial transcription initiation transitional complex, TC8

SM: ATP

9mn9

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Structure of the human mitochondrial promoter-initiated transcription elongation complex, P-EC13

SM: CH1

9mna

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Structure of the human mitochondrial promoter-initiated transcription elongation complex with TEFM, pEC9-TEFM

SM: ATP

9n5c

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RNA polymerase II elongation complex with 8-oxoG at +1 site, CMPCPP-bound

SM: 2TM

9n5e

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RNA polymerase II elongation complex with 8-oxoG at +1 site, AMPCPP in E-site

SM: APC

9n5g

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RNA polymerase II elongation complex with 8-oxoG at +1 site, ATP in both A- and E-site

SM: ATP

9nl2

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

SM: TTP

9nl3

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

SM: TTP

9ol2

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RNA-imidazolium-bridged dinucleotide intermediate complex

SM: EQ1

9ol3

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DNA-imidazolium-bridged dinucleotide intermediate complex

9pvx

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RNA polymerase II elongation complex with dA at +1 site, 8-oxo-GTP bound in E-site.

SM: 8GT

9pyz

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SARS-CoV-2 core polymerase complex bound to RNA, araUMP, and UTP

SM: UTP

9yd3

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RNA primer non-enzymatic extension product with RNA substrate

SM: EQ4

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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

RNA/DNA/Protein

RNA/Protein

Source organism

Betacoronavirus

Homo

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

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

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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

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