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)

196 Complexes found

Complexes per page

60 120 180

filters used: RNA environment global: RNA/DNA/Protein

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Structure of Yeast RNA polymerase II elongation complex with ATP frame-14

SM: ATP

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Structure of Yeast RNA polymerase II elongation complex with ATP frame-15

SM: ATP

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Structure of Yeast RNA polymerase II elongation complex with ATP frame-16

SM: ATP

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Structure of Yeast RNA polymerase II elongation complex with ATP frame-17

SM: ATP

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Structure of Yeast RNA polymerase II elongation complex with ATP frame-18

SM: ATP

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Structure of Yeast RNA polymerase II elongation complex with ATP frame-19

SM: ATP

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Structure of Yeast RNA polymerase II elongation complex with ATP frame-20

SM: ATP

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Cryo-EM structure of the catalytic core of human telomerase at the initiation state of the repeat addition cycle

SM: 1GC

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Cryo-EM structure of the catalytic core of human telomerase at the elongation state of the repeat addition cycle

SM: A1ACD

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Cryo-EM structure of the catalytic core of human telomerase at the pre-termination state of the repeat addition cycle

SM: 1GC

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CryoEM structure of transcribing RNA polymerase II elongation complex with ATP and Elf1

SM: ATP

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CryoEM structure of the T.thermophilus transcription initiation complex bound to Gp4A-C-U and CTP, -1 dC in the template DNA strand

SM: CTP

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Cryo-EM structure of substrate-bound DRT9 hexamer complex

SM: DTP

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De novo initial transcribing RNA polymerase with 2-mer RNA and bound CTP / Michaelis complex (RPitc2+CTP)

SM: CTP

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Cryo-EM structure of Escherichia coli transcription initiation complex with GpA and pseudouridimycin (PUM)

SM: PUM

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Cryo-EM structure of Escherichia coli transcription initiation complex with GpA and des-hydroxy pseudouridimycin (des-hydroxy PUM)

SM: A1CYH

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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/Protein

Source organism

Bombyx

Escherichia

Haloarcula

Homo

Klebsiella

Mycobacterium

Saccharomyces

Taeniopygia

Teseptimavirus

Thermus

Tribolium

Trichoplusia

Molecular weight

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Number of atoms

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Number of PDB entries

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Number of interacting chains

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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]

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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]

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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

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Volume

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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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HARIBOSS

Complexes

9sby

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9sbz

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9sc0

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9sc1

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9sc2

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9sc3

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9sc4

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9shy

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9shz

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9si0

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9sv6

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9ukt

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9vma

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9ymu

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9ynp

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9ynq

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