HARIBOSS

Harnessing RIBOnucleic acid - Small molecules Structures

Compounds
RNA-SM complexes
About

You are here

Complexes

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)

1894 Complexes found

Complexes per page

60 120 180

filters used: With equivalence class

9uht

Select this complex

SARS-CoV-2 E-RTC in complex with RNA-nsp9 and GMPPNP

SM: GNP

9ukt

Select this complex

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

9uw0

Select this complex

Crystal structure of 2'-dG-III riboswitch with Guanosine, manganese saok

SM: GMP

9uwh

Select this complex

human mitoribosome trapped by retapamulin

9v26

Select this complex

Cryo- EM structure of 75S ribosome with A/P- & P/E- tRNAs from Entamoeba histolytica bound to antibiotic paromomycin

SM: PAR

9v29

Select this complex

Cryo- EM structure of small subunit (body) of 75S ribosome with A/P- & P/E- tRNAs from Entamoeba histolytica bound to antibiotic paromomycin

SM: PAR

9v4u

Select this complex

Crystal structure of Guanine-II riboswitch in complex with 7,8-dihydroneopterin

SM: NPR

9v4v

Select this complex

Crystal structure of Guanine-II riboswitch in complex with isoxanthopterin

SM: 7PD

9v4y

Select this complex

Crystal structure of Guanine-II riboswitch in complex with 8-aminoguanine

SM: ANG

9v4z

Select this complex

Crystal structure of Guanine-II riboswitch in complex with 8-oxoguanine

SM: OXG

9v50

Select this complex

Crystal structure of Guanine-II riboswitch in complex with 8-methylguanine

9v51

Select this complex

Crystal structure of Guanine-II riboswitch in complex with tetrahydrobiopterin

SM: H4B

9v7n

Select this complex

Cryo-EM structures of the Azoarcus pre-tRNA(ILE) conformation a undergoing the first-step self-splicing

SM: GMP

9v7o

Select this complex

Cryo-EM structures of the Azoarcus pre-tRNA(ILE) conformation b undergoing the first-step self-splicing

SM: GMP

9vma

Select this complex

Cryo-EM structure of substrate-bound DRT9 hexamer complex

SM: DTP

9vmz

Select this complex

Crystal structure of Broccoli aptamer in with BI

9vxm

Select this complex

Human mitoribosome in a non-rotated state, with multiple neomycin molecules bound, featuring A/A-site and P/P-site tRNAs

SM: NAD NMY SPM

9vxn

Select this complex

Human cytosolic ribosome in a rotated state, with multiple neomycin molecules bound, featuring A/P-site and P/E-site tRNAs

SM: NMY

9xe6

Select this complex

Crimean-Congo hemorrhagic fever virus RNA polymerase containing a 10-bp RNA product and incorporated 2FC

SM: 2KH

9xe7

Select this complex

Crimean-Congo hemorrhagic fever virus RNA polymerase containing a 10-bp RNA product and incorporated cytidine

SM: 2KH

9xe9

Select this complex

Crimean-Congo hemorrhagic fever virus RNA polymerase containing a 15-bp RNA product

SM: 2KH

9xec

Select this complex

Crimean-Congo hemorrhagic fever virus RNA polymerase containing a 9-bp RNA product

SM: 2KH

9yd3

Select this complex

RNA primer non-enzymatic extension product with RNA substrate

SM: EQ4

9yd4

Select this complex

RNA primer non-enzymatic extension product with DNA substrate

9ymu

Select this complex

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

SM: CTP

9ynp

Select this complex

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

SM: PUM

9ynq

Select this complex

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

9z2n

Select this complex

CryoEM structure of human NSUN2(C271A) with SAH cross-linked to tRNA Lys(CTT) (D-arm conformation)

SM: SAH

9z2o

Select this complex

CryoEM structure of human NSUN2(C271A) with SAH cross-linked to tRNA Lys(CTT) (No D-arm conformation)

SM: SAH

9z2r

Select this complex

CryoEM structure of human NSUN2 with tRNA Lys(CTT) and SFG (D-arm conformation)

SM: SFG

9z2t

Select this complex

CryoEM structure of human NSUN2 with tRNA Lys(CTT) and SFG (No D-arm conformation)

SM: SFG

9z2u

Select this complex

CryoEM structure of human NSUN2(C271A) with SAH cross-linked to tRNA Lys(TTT) (D-arm conformation)

SM: SAH

9z2w

Select this complex

CryoEM structure of human NSUN2(C271A) with SAH cross-linked to tRNA Lys(TTT) (No D-arm conformation)

SM: SAH

9z3d

Select this complex

CryoEM structure of human NSUN2(C271A) with SAH cross-linked to a pre-tRNA Leu(CAA) intron

SM: SAH

Previous
32 of 32
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

RNA/DNA

RNA/DNA/Protein

RNA/Protein

Source organism

Acidobacterium

Acinetobacter

Alphainfluenzavirus

Alpharetrovirus

Anabaena

Arabidopsis

Archaeoglobus

Azoarcus

Bacillus

Bacteroides

Bandavirus

Betacoronavirus

Betainfluenzavirus

Bifidobacterium

Bombyx

Bos

Brassica

Caenorhabditis

Caldanaerobacter

Candida

Candidatus Korobacter

Candidatus Pelagibacter

Carnobacterium

Chlamydomonas

Clostridium

Coxiella

Cutibacterium

Cypovirus

Deinococcus

Desulfonema

Didymium

Entamoeba

Enterococcus

Enterovirus

Escherichia

Faecalibacterium

Francisella

Fusobacterium

Geobacter

Giardia

Gloeobacter

Halalkalibacterium (ex Joshi et al. 2022)

Haloarcula

Henipavirus

Hepacivirus

Homo

Ideonella

Klebsiella

Kluyveromyces

Lacticaseibacillus

Lactococcus

Leishmania

Lentivirus

Listeria

Mammarenavirus

Mesoplasma

Mesorhizobium

Mus

Mycobacterium

Mycolicibacterium

Mycoplasmoides

Neurospora

Nicotiana

Oceanobacillus

Orthobunyavirus

Orthoflavivirus

Orthonairovirus

Orthopneumovirus

Orthoreovirus

Oryctolagus

Paenibacillus

Plasmodium

Porphyromonas

Pseudomonas

Pylaiella

Pyrobaculum

Ralstonia

Rauchvirus

Roseobacter

Rotavirus

Ruminococcus

Saccharolobus

Saccharomyces

Schaalia

Segatella

Solanum

Staphylococcus

Streptococcus

Streptomyces

Sulfobacillus

Sulfolobus

Sus

Syntrophothermus

Taeniopygia

Tequatrovirus

Tetrahymena

Thermoanaerobacter

Thermochaetoides

Thermotoga

Thermovirga

Thermus

Thogotovirus

Tilapinevirus

Tribolium

Trichoplusia

Triticum

Trypanosoma

Tymovirus

Varicellovirus

Vesiculovirus

Vibrio

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

About
Contact
Credits
Policies

Loading...