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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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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)

218 RNA-SM complexes found

RNA-SM complexes per page

60 120 180

filters used: RNA family global: synthetic construct

Structure of complex 9bdd

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

Structure of complex 9blf

9blf

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SARS-CoV-2 core polymerase complex inhibited by araCTP

SM: HF4

Structure of complex 9j6p

9j6p

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

SM: A1L3Y A1L3Y

Structure of complex 9ja1

9ja1

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The RNA polymerase II elongation complex from Saccharomyces cerevisiae

SM: ATP

Structure of complex 9ljr

9ljr

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

Structure of complex 9ljs

9ljs

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

Structure of complex 9ljt

9ljt

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

Structure of complex 9lju

9lju

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

Structure of complex 9ljv

9ljv

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

Structure of complex 9ljw

9ljw

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

SM: GDP

Structure of complex 9mn6

9mn6

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

SM: ATP

Structure of complex 9mn7

9mn7

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

SM: ATP

Structure of complex 9mn8

9mn8

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Structure of the human mitochondrial transcription initiation transitional complex, TC8

SM: ATP

Structure of complex 9mn9

9mn9

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

SM: CH1

Structure of complex 9mna

9mna

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

SM: ATP

Structure of complex 9n5c

9n5c

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

SM: 2TM

Structure of complex 9n5e

9n5e

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

SM: APC

Structure of complex 9n5g

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

Structure of complex 9nl2

9nl2

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

SM: TTP

Structure of complex 9nl3

9nl3

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

SM: TTP

Structure of complex 9ol2

9ol2

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RNA-imidazolium-bridged dinucleotide intermediate complex

Structure of complex 9ol3

9ol3

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DNA-imidazolium-bridged dinucleotide intermediate complex

SM: A1CGJ A1CGJ

Structure of complex 9pck

9pck

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Human DNA Polymerase Gamma-RNA-DNA Primer-Template Complex with Incoming ATP

SM: TTP

Structure of complex 9pvx

9pvx

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

SM: 8GT

Structure of complex 9pyz

9pyz

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

SM: UTP

Structure of complex 9yd3

9yd3

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RNA primer non-enzymatic extension product with RNA substrate

Structure of complex 9zwr

9zwr

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Crystal structure of the N4BP2 polynucleotide kinase domain complexed with ATP or ADP, Mg, and the trinucleotide substrate AAA or its 5'-phosphorylated product pAAA.

Structure of complex 9zws

9zws

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Crystal structure of the N4BP2 polynucleotide kinase domain complexed with ATP or ADP, Mg, and the trinucleotide substrate ACA or its 5'-phosphorylated product pACA.

Structure of complex 9zwt

9zwt

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Crystal structure of the N4BP2 polynucleotide kinase domain complexed with ATP or ADP, Mg, and the trinucleotide substrate AGA or its 5'-phosphorylated product pAGA.

Structure of complex 9zwu

9zwu

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Crystal structure of the N4BP2 polynucleotide kinase domain complexed with ATP or ADP, Mg, and the trinucleotide substrate AUA or its 5'-phosphorylated product pAUA.

Structure of complex 9zwv

9zwv

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Crystal structure of the N4BP2 polynucleotide kinase domain complexed with ATP, Mg, and the trinucleotide substrate CAA.

SM: ATP ATP ATP

Structure of complex 9zww

9zww

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Crystal structure of the N4BP2 polynucleotide kinase domain complexed with ATP, Mg, and the trinucleotide substrate CCA.

SM: ATP ATP ATP

Structure of complex 9zwx

9zwx

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Crystal structure of the N4BP2 polynucleotide kinase domain complexed with ATP, Mg, and the trinucleotide substrate CGA.

SM: ATP ATP ATP

Structure of complex 9zwy

9zwy

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Crystal structure of the N4BP2 polynucleotide kinase domain complexed with ATP, Mg, and the trinucleotide substrate CUA.

SM: ATP ATP ATP

Structure of complex 9zwz

9zwz

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Crystal structure of the N4BP2 polynucleotide kinase domain complexed with ATP or ADP, Mg, and the trinucleotide substrate GAA or its 5'-phosphorylated product pGAA.

SM: ATP

Structure of complex 9zx3

9zx3

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Crystal structure of the N4BP2 polynucleotide kinase domain complexed with ATP or ADP, Mg, and the trinucleotide substrate UAA ot its 5'-phosphorylated product pUAA

SM: ATP ATP ATP

Structure of complex 9zx5

9zx5

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Crystal structure of the N4BP2 polynucleotide kinase domain complexed with ATP or ADP, Mg, and the trinucleotide substrate UGA.

SM: ATP ATP ATP

Structure of complex 9zx6

9zx6

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Crystal structure of the N4BP2 polynucleotide kinase domain complexed with ATP, Mg, and the trinucleotide substrate UUA.

SM: ATP ATP ATP

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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)

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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/DNA/Protein

RNA/Protein

Source organism

Betacoronavirus

Homo

Molecular weight (complex)

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Filter entries " Molecular weight (complex) " between the two values. Global DB range: 0 – 13090

Number of atoms

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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/DNA/Protein

RNA/Other

RNA/Protein

RNA environment detailed

DNA

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

synthetic construct

unknown

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