HARIBOSS

Harnessing RIBOnucleic acid - Small molecules Structures

Compounds
RNA-SM complexes
About

You are here

Complexes

× Close

System Properties

Experimental technique Experimental resolution Molecular weight Deposition date Molecule type Organism

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 Non-redundant only

862 Complexes found

Complexes per page

60 120 180

Select this complex

20A Mutant c-di-GMP Vc2 Riboswitch bound with 3',3'-cGAMP

SM: 4BW

Select this complex

High-resolution structure of the Escherichia coli ribosome

SM: 1PE PG4

Select this complex

Crystal structure of the 30S ribosomal subunit from Thermus thermophilus in complex with tigecycline

SM: T1C

Select this complex

Crystal structure of the Thermus thermophilus 70S ribosome in complex with antibiotic A201A, mRNA and three tRNAs in the A, P and E sites at 2.65A resolution

SM: 4M2

Select this complex

Paromomycin bound to a leishmanial ribosomal A-site

SM: PAR

Select this complex

Crystal structure of the Onc112 antimicrobial peptide bound to the Thermus thermophilus 70S ribosome

SM: ARG

Select this complex

The structure of A pfI Riboswitch Bound to ZMP

SM: AMZ

Select this complex

Complex of Thermous thermophilus ribosome bound to BipA-GDPCP

SM: NMY

Select this complex

Complex of Thermous thermophilus ribosome (A-and P-site tRNA) bound to BipA-GDPCP

SM: 8AN NMY

Select this complex

2.9A Structure of E. coli ribosome-EF-TU complex by cs-corrected cryo-EM

SM: FME

Select this complex

Crystal structure of the Corn RNA aptamer in complex with DFHO, site-specific 5-iodo-U

SM: 747

Select this complex

Crystal structure of the Corn RNA aptamer in complex with DFHO, iridium hexammine soak

SM: 747

Select this complex

Ambient-temperature crystal structure of 30S ribosomal subunit from Thermus thermophilus in complex with paromomycin

SM: PAR

Select this complex

Fusobacterium ulcerans ZTP riboswitch bound to ZMP

SM: AMZ

Select this complex

Selective Small Molecule Inhibition of the FMN Riboswitch

SM: 51B

Select this complex

PreQ1-II riboswitch with an engineered G-U wobble pair bound to Cs+

SM: PRF

Select this complex

Coping with proline stalling: structural basis of hypusine-induced protein synthesis by the eukaryotic ribosome

SM: SPS

Select this complex

Cooperativity and Downstream Binding in RNA Replication

SM: 5GP

Select this complex

Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with hygromycin A

SM: HGR

Select this complex

Crystal structure of the Thermus thermophilus 70S ribosome in complex with Hygromycin-A at 3.1A resolution

SM: HGR

Select this complex

Crystal structure of the Thermus thermophilus 70S ribosome in complex with antibiotic Hygromycin A, mRNA and three tRNAs in the A, P and E sites at 2.6A resolution

SM: HGR

Select this complex

Structure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with a U-U mismatch in the first position and antibiotic paromomycin

SM: PAR

Select this complex

Structure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with a U-U mismatch in the second position and antibiotic paromomycin

SM: PAR

Select this complex

Structure of the anisomycin-containing uL3 W255C mutant 80S yeast ribosome

SM: ANM

Select this complex

SAM-I riboswitch bearing the H. marismortui Kt-7 variant C-2bU

SM: SAM

Select this complex

SAM-I riboswitch bearing the H. marismortui Kt-7 variant 3bn is UG

SM: SAM

Select this complex

SAM-I riboswitch bearing the H. marismortui Kt-7 variant 3bn is GG

SM: SAM

Select this complex

SAM-I riboswitch bearing the H. marismortui Kt-7 variant 3bn is CC

SM: SAM

Select this complex

SAM-I riboswitch bearing the H. marismortui Kt-7 variant 3bn is UU

SM: SAM

Select this complex

SAM-I riboswitch bearing the H. marismortui Kt-7 variant 3bn is AA

SM: SAM

Select this complex

SAM-I riboswitch bearing the H. marismortui Kt-7 variant 3bn is CA

SM: SAM

Select this complex

SAM-I riboswitch bearing the H. marismortui Kt-7 variant 3bn is UA

SM: SAM

Select this complex

SAM-I riboswitch bearing the H. marismortui Kt-7 variant 3bn is GU

SM: SAM

Select this complex

SAM-I riboswitch bearing the H. marismortui Kt-7 variant 3bn is UC

SM: SAM

Select this complex

SAM-I riboswitch bearing the H. marismortui Kt-7 variant 3bn is CG

SM: SAM

Select this complex

SAM-I riboswitch bearing the H. marismortui Kt-7 variant 3bn is CU

SM: SAM

Select this complex

RNA primer-template complex with 2-methylimidazole-activated monomer analogue

SM: PZG

Select this complex

The crystal structure of the large ribosomal subunit of Staphylococcus aureus in complex with lefamulin

SM: 62B

Select this complex

Structure of T. thermophilus 70S ribosome complex with mRNA, tRNAfMet, near-cognate tRNALys with U-G mismatch in the A-site and antibiotic paromomycin

SM: PAR SPE

Select this complex

Structure of T. thermophilus 70S ribosome complex with mRNA, tRNAfMet and near-cognate tRNALys with U-G mismatch in the A-site

SM: SPE

Select this complex

Structure of T. thermophilus 70S ribosome complex with mRNA, tRNAfMet and cognate tRNAVal in the A-site

SM: SPE

Select this complex

Structure of RelA bound to the 70S ribosome

SM: PAR

Select this complex

High-resolution structure of the Escherichia coli ribosome

SM: 1PE PG4

Select this complex

Structure of the WT E coli ribosome bound to tetracycline

SM: 1PE PG4 TAC

Select this complex

Structure of the 70S E coli ribosome with the U1052G mutation in the 16S rRNA bound to tetracycline

SM: 1PE PG4 TAC

Select this complex

Structure of the E coli 70S ribosome with the U1060A mutation in 16S rRNA

SM: 1PE PG4

Select this complex

Structure of the E coli 70S ribosome with the U1052G mutation in 16S rRNA bound to tigecycline

SM: 1PE PG4 T1C

Select this complex

Structure of the Wild-type 70S E coli ribosome bound to Tigecycline

SM: 1PE PG4 T1C

Select this complex

Structure of the Escherichia coli ribosome with the U1052G mutation in the 16S rRNA

SM: 1PE PG4

Select this complex

Structure of a 5-hydroxytryptophan aptamer

SM: 4PQ

Select this complex

RNA 15mer duplex binding with PZG monomer

SM: PZG

Select this complex

Selective Small Molecule Inhibition of the FMN Riboswitch

SM: 6YG

Select this complex

Solution NMR structure of the GTP binding Class II RNA aptamer-ligand-complex containing a protonated adenine nucleotide with a highly shifted pKa.

SM: GTP

Select this complex

Crystal structure of Agelastatin A bound to the 80S ribosome

SM: 7MB

Select this complex

Crystal structure of geneticin (G418) bound to the yeast 80S ribosome

SM: GET

Select this complex

Crystal structure of aminoglycoside TC007 in complex with 70S ribosome from Thermus thermophilus, three tRNAs and mRNA (soaking)

SM: 8UZ

Select this complex

Crystal structure of aminoglycoside TC007 co-crystallized with 70S ribosome from Thermus thermophilus, three tRNAs and mRNA

SM: 8UZ

Select this complex

Crystal structure of Paromomycin bound to the yeast 80S ribosome

SM: PAR

Select this complex

Crystal structure of aminoglycoside TC007 bound to the yeast 80S ribosome

SM: 8UZ

Select this complex

The crystal structure of the large ribosomal subunit of Staphylococcus aureus in complex with RB02

SM: 95H

Previous
7 of 15
Next
Go to page

Experimental method

Electron Microscopy

Solution NMR

X-ray

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

Arabidopsis

Bacillus

Bifidobacterium

Caldanaerobacter

Candida

Candidatus Koribacter

Candidatus Pelagibacter

Clostridium

Cutibacterium

Deinococcus

Didymium

Enterovirus

Escherichia

Faecalibacterium

Fusobacterium

Geobacter

Gloeobacter

Haloarcula

Hepacivirus

Homo

Ideonella

Lacticaseibacillus

Lactococcus

Leishmania

Lentivirus

Listeria

Mesoplasma

Mesorhizobium

Mus

Mycobacterium

Mycolicibacterium

Mycoplasmoides

Nicotiana

Oceanobacillus

Oryctolagus

Pseudomonas

Pylaiella

Ralstonia

Roseobacter

Ruminococcus

Saccharomyces

Schaalia

Staphylococcus

Streptococcus

Sulfobacillus

Sus

Syntrophothermus

Tetrahymena

Thermoanaerobacter

Thermotoga

Thermovirga

Thermus

Tymovirus

Varicellovirus

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

25-28 Rue du Dr Roux, 75015 Paris

01 45 68 80 00

About
Contact
Credits