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

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

998 Complexes found

Complexes per page

60 120 180

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HIV-2 TAR-ARGININAMIDE COMPLEX, NMR, 20 STRUCTURES

SM: ARG

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HIV-2 TRANS ACTIVATING REGION RNA COMPLEX WITH ARGININAMIDE, NMR, MINIMIZED AVERAGE STRUCTURE

SM: ARG

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AMP RNA APTAMER COMPLEX, NMR, 8 STRUCTURES

SM: AMP

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ARG-BOUND TAR RNA, NMR

SM: ARG

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THEOPHYLLINE-BINDING RNA IN COMPLEX WITH THEOPHYLLINE, NMR, 10 STRUCTURES

SM: TEP

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STRUCTURAL BASIS FOR RECOGNITION OF THE RNA MAJOR GROOVE IN THE TAU EXON 10 SPLICING REGULATORY ELEMENT BY AMINOGLYCOSIDE ANTIBIOTICS

SM: NMY

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CRYSTAL STRUCTURE OF YEAST PHENYLALANINE TRANSFER RNA AT 2.0 A RESOLUTION

SM: SPM

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CRYSTAL STRUCTURE OF THE MALACHITE GREEN APTAMER COMPLEXED WITH TETRAMETHYL-ROSAMINE

SM: ROS

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CRYSTAL STRUCTURE OF A BIOTIN-BINDING RNA PSEUDOKNOT

SM: BTN

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SOLUTION STRUCTURE OF FMN-RNA APTAMER COMPLEX, NMR, 5 STRUCTURES

SM: FMN

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CRYSTAL STRUCTURE OF A 14BP RNA OLIGONUCLEOTIDE CONTAINING DOUBLE UU BULGES: A NOVEL INTRAMOLECULAR U*(AU) BASE TRIPLE

SM: SPM

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EUKARYOTIC DECODING REGION A-SITE RNA-PAROMOMYCIN COMPLEX

SM: PAR

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STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNIT IN COMPLEX WITH TETRACYCLINE

SM: TAC

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STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNIT IN COMPLEX WITH HYGROMYCIN B

SM: HYG

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1.66 A STRUCTURE OF A-DUPLEX WITH BULGED ADENOSINE, SPERMINE FORM

SM: SPM

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CRYSTAL STRUCTURE OF THE 30S RIBOSOMAL SUBUNIT FROM THERMUS THERMOPHILUS IN COMPLEX WITH EDEINE

SM: EDE

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CRYSTAL STRUCTURE OF THE 30S RIBOSOMAL SUBUNIT FROM THERMUS THERMOPHILUS IN COMPLEX WITH TETRACYCLINE

SM: TAC

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CRYSTAL STRUCTURE ANALYSIS OF A TRNA-NEOMYCIN COMPLEX

SM: NMY

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STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNIT IN COMPLEX WITH THE ANTIBIOTIC PAROMOMYCIN

SM: PAR

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STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNIT IN COMPLEX WITH A MESSENGER RNA FRAGMENT AND COGNATE TRANSFER RNA ANTICODON STEM-LOOP BOUND AT THE A SITE AND WITH THE ANTIBIOTIC PAROMOMYCIN

SM: PAR

1j5a

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STRUCTURAL BASIS FOR THE INTERACTION OF ANTIBIOTICS WITH THE PEPTIDYL TRANSFERASE CENTER IN EUBACTERIA

SM: CTY

1j7t

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Complex between Paromomycin and the 16S-rRNA A-site at 2.5 A resolution

SM: PAR

1j8g

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X-ray Analysis of a RNA Tetraplex r(uggggu)4 at Ultra-High Resolution

SM: SPM

1jzx

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Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Center in Eubacteria

SM: CLY

1jzy

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Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Center in Eubacteria

SM: ERY

1jzz

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Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Center in Eubacteria

SM: ROX

1k01

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Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Center in Eubacteria

SM: CLM

1k73

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Co-crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit

SM: ANM

1koc

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RNA APTAMER COMPLEXED WITH ARGININE, NMR

SM: ARG

1kod

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RNA APTAMER COMPLEXED WITH CITRULLINE, NMR

SM: CIR

1lc4

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Crystal Structure of Tobramycin Bound to the Eubacterial 16S rRNA A Site

SM: TOY

1lvj

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STRUCTURE OF TAR RNA COMPLEXED WITH A TAT-TAR INTERACTION NANOMOLAR INHIBITOR THAT WAS IDENTIFIED BY COMPUTATIONAL SCREENING

SM: PMZ

1m90

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Co-crystal structure of CCA-Phe-caproic acid-biotin and sparsomycin bound to the 50S ribosomal subunit

SM: SPS

1mwl

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Crystal structure of geneticin bound to the eubacterial 16S rRNA A site

SM: GET

1n32

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Structure of the Thermus thermophilus 30S ribosomal subunit bound to codon and near-cognate transfer RNA anticodon stem-loop mismatched at the first codon position at the a site with paromomycin

SM: PAR

1n33

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Structure of the Thermus thermophilus 30S ribosomal subunit bound to codon and near-cognate transfer rna anticodon stem-loop mismatched at the second codon position at the a site with paromomycin

SM: PAR

1n7a

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RIP-Radiation-damage Induced Phasing

SM: SPM

1n7b

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RIP-Radiation-damage Induced Phasing

SM: SPM

1n8r

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Structure of large ribosomal subunit in complex with virginiamycin M

SM: VIR

1nji

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Structure of chloramphenicol bound to the 50S ribosomal subunit

SM: CLM

1njm

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The crystal structure of the 50S Large ribosomal subunit from Deinococcus radiodurans complexed with a tRNA acceptor stem mimic (ASM) and the antibiotic sparsomycin

SM: SPS

1njn

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The crystal structure of the 50S Large ribosomal subunit from Deinococcus radiodurans complexed with the antibiotic sparsomycin

SM: SPS

1nta

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2.9 A crystal structure of Streptomycin RNA-aptamer

SM: SRY

1ntb

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2.9 A crystal structure of Streptomycin RNA-aptamer complex

SM: SRY

1nwx

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COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH ABT-773

SM: 773

1o15

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THEOPHYLLINE-BINDING RNA IN COMPLEX WITH THEOPHYLLINE, NMR, REGULARIZED MEAN STRUCTURE, REFINEMENT WITH TORSION ANGLE AND BASE-BASE POSITIONAL DATABASE POTENTIALS AND DIPOLAR COUPLINGS

SM: TEP

1p9x

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THE CRYSTAL STRUCTURE OF THE 50S LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS COMPLEXED WITH TELITHROMYCIN KETOLIDE ANTIBIOTIC

SM: TEL

1q8n

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Solution Structure of the Malachite Green RNA Binding Aptamer

SM: MGR

1raw

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ATP BINDING RNA APTAMER IN COMPLEX WITH AMP, NMR, 10 STRUCTURES

SM: AMP

1tn1

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CRYSTALLOGRAPHIC AND BIOCHEMICAL INVESTIGATION OF THE LEAD(II)-CATALYZED HYDROLYSIS OF YEAST PHENYLALANINE TRNA

SM: SPM

1tn2

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CRYSTALLOGRAPHIC AND BIOCHEMICAL INVESTIGATION OF THE LEAD(II)-CATALYZED HYDROLYSIS OF YEAST PHENYLALANINE T-RNA

SM: SPM

1uts

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Designed HIV-1 TAR Binding Ligand

SM: P13

1uud

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NMR structure of a synthetic small molecule, rbt203, bound to HIV-1 TAR RNA

SM: P14

1uui

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NMR structure of a synthetic small molecule, rbt158, bound to HIV-1 TAR RNA

SM: P12

1vvj

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Crystal Structure of Frameshift Suppressor tRNA SufA6 bound to Codon CCC-G on the Ribosome

SM: PAR

1xbp

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Inhibition of peptide bond formation by pleuromutilins: The structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with Tiamulin

SM: MUL

1xmo

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Crystal Structure of mnm5U34t6A37-tRNALysUUU Complexed with AAG-mRNA in the Decoding Center

SM: PAR

1xnq

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Structure of an Inosine-Adenine Wobble Base Pair Complex in the Context of the Decoding Center

SM: PAR

1xnr

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Crystal Structure of an Inosine-Cytosine Wobble Base Pair in the Context of the Decoding Center

SM: PAR

1xpf

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HIV-1 subtype A genomic RNA Dimerization Initiation Site

SM: SPM

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Experimental method

Electron Microscopy

Solution NMR

X-ray

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

RNA/DNA/Protein

RNA/Protein

Source organism

Acidobacterium

Acinetobacter

Alpharetrovirus

Arabidopsis

Bacillus

Bifidobacterium

Caldanaerobacter

Candida

Candidatus Korobacter

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

Pyrobaculum

Ralstonia

Roseobacter

Ruminococcus

Saccharolobus

Saccharomyces

Schaalia

Staphylococcus

Streptococcus

Streptomyces

Sulfobacillus

Sus

Syntrophothermus

Tequatrovirus

Tetrahymena

Thermoanaerobacter

Thermotoga

Thermovirga

Thermus

Tymovirus

Varicellovirus

Vibrio

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

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SiteScore

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Dscore

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Exposure

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Enclosure

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Hydrophobicity

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Hydrophilicity

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Donor/Acceptor

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Volume

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