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

862 Complexes found

Complexes per page

60 120 180

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Wild-type Escherichia coli ribosome with antibiotic radezolid

SM: RD8

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Crystal structure of Pepper RNA aptamer in complex with HBC ligand and Fab BL3-6

SM: J8F

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Crystal structure of an E. coli thiM riboswitch bound to thiamine, manganese ions

SM: VIB

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Crystal structure of the E. coli thiM riboswitch in complex with thiamine pyrophosphate, manganese ions

SM: TPP

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Crystal structure of the E. coli thiM riboswitch in complex with thiamine bisphosphonate, manganese ions

SM: GMI

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Crystal structure of the E. coli thiM riboswitch in complex with thiamine bisphosphonate, calcium ions

SM: GMI

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CryoEM structure of the human 40S small ribosomal subunit in complex with translation initiation factors eIF1A and eIF5B.

SM: 5GP

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Crystal structure of the E. coli thiM riboswitch bound to N-methyl-1-(quinoxalin-6-yl)methanamine (compound 16)

SM: KWU

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Crystal structure of the E. coli thiM riboswitch in complex with N1,N1-dimethyl-N2-(quinoxalin-6-ylmethyl)ethane-1,2-diamine (linked compound 37)

SM: KXC

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Crystal structure of the E. coli thiM riboswitch bound to 1-(4-(piperazin-1-yl)pyridin-3-yl)-N-(quinoxalin-6-ylmethyl)methanamine (linked compound 38)

SM: KWL

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Crystal structure of Pepper RNA aptamer in complex with HBC599 ligand and Fab BL3-6

SM: KY6

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Crystal structure of the Thermus thermophilus 70S ribosome in complex with mRNA, aminoacylated A-site Gly-NH-tRNAgly, aminoacylated P-site fMet-NH-tRNAmet, deacylated E-site tRNAgly, and chloramphenicol at 2.55A resolution

SM: CLM

7u87

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Product of 13mer primer with activated G monomer diastereomer 1

SM: LXI

7u88

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Product of 13mer primer with activated G monomer diastereomer 2

SM: LXI

7u89

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Product of 14mer primer with activated G monomer diastereomer 1

SM: LXI

7u8a

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Product of 14mer primer with activated G monomer diastereomer 2

SM: LXI

7u8b

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Product of 14mer primer with activated asymmetric GA dimer diastereomer 1

SM: LXR

7ucj

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Mammalian 80S translation initiation complex with mRNA and Harringtonine

SM: MQ6

7uck

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80S translation initiation complex with ac4c(-1) mRNA and Harringtonine

SM: MQ6

7uoo

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Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state

SM: B3P

7uqb

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Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a SPB1-D52A strain with AlF4

SM: B3P

7uqz

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Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a SPB1 D52A strain

SM: B3P

7uvy

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A. baumannii ribosome-Streptothricin-D complex: 70S with P-site tRNA

SM: OIY

7uvz

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A. baumannii ribosome-Streptothricin-D complex: 70S with E-site tRNA

SM: OIY

7uw1

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A. baumannii 70S ribosome-Streptothricin-D complex

SM: OIY

7v08

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Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a Spb1 D52A suppressor 3 strain

SM: B3P

7wib

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The THF-II riboswitch bound to THF

SM: THG

7wif

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The THF-II riboswitch bound to H4B

SM: H4B

7wii

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The THF-II riboswitch bound to NPR

SM: NPR

7yc8

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Cryo-EM structure of Tetrahymena ribozyme conformation 1 undergoing the first-step self-splicing

SM: GTP

7ycg

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Cryo-EM structure of Tetrahymena ribozyme conformation 2 undergoing the first-step self-splicing

SM: GTP

7ych

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Cryo-EM structure of Tetrahymena ribozyme conformation 3 undergoing the first-step self-splicing

SM: GTP

7yci

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Cryo-EM structure of Tetrahymena ribozyme conformation 4 undergoing the first-step self-splicing

SM: GTP

7zj4

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Ligand bound state of a brocolli-pepper aptamer FRET tile

SM: 1TU J93

8a3d

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Human mature large subunit of the ribosome with eIF6 and homoharringtonine bound

SM: HMT

8a5i

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Cryo-EM structure of Lincomycin bound to the Listeria monocytogenes 50S ribosomal subunit.

SM: 3QB

8akn

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Cryo-EM structure of the proline-rich antimicrobial peptide drosocin bound to the terminating ribosome

SM: SPM

8am9

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Cryo-EM structure of the proline-rich antimicrobial peptide drosocin bound to the elongating ribosome

SM: SPM

8ana

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Cryo-EM structure of the proline-rich antimicrobial peptide drosocin bound to the 50S ribosomal subunit

SM: SPM

8any

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Human mitochondrial ribosome in complex with LRPPRC, SLIRP, A-site, P-site, E-site tRNAs and mRNA

SM: SPM

8auv

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Cryo-EM structure of the plant 40S subunit

SM: SPM

8aye

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E. coli 70S ribosome bound to thermorubin and fMet-tRNA

SM: T8B

8b2l

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Cryo-EM structure of the plant 80S ribosome

SM: SPM

8btk

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Structure of the TRAP complex with the Sec translocon and a translating ribosome

SM: SPM

8c3a

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Crystal structure of ailanthone bound to the Candida albicans 80S ribosome

SM: TIX

8ca7

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Omadacycline and spectinomycin bound to the 30S ribosomal subunit head

SM: U3B

8cai

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Streptomycin and Hygromycin B bound to the 30S body

SM: HY0

8ceu

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Retapamulin and Capreomycin bound to the 50S subunit

SM: G34

8cf1

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Tetracycline bound to the 30S head

SM: TAC

8cf2

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Solution structure of the RNA helix formed by the 5'-end of U1 snRNA and an A-1 bulged 5'-splice site in complex with SMN-CY

SM: ULR

8cf8

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Eravacycline bound to the 30S head

SM: YQM

8cgd

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Clindamycin bound to the 50S subunit

SM: CLY

8cgi

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Pentacycline TP038 bound to the 30S head

SM: P8F

8cgj

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Streptomycin bound to the 30S body

SM: TAC

8cgk

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Lincomycin and Avilamycin bound to the 50S subunit

SM: 3QB

8cgr

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Apramycin bound to the 30S body

SM: AM2

8cgu

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Gentamicin bound to the 30S body

SM: LLL

8cgv

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Tiamulin bound to the 50S subunit

SM: MUL

8crx

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Cutibacterium acnes 70S ribosome with mRNA, P-site tRNA and Sarecycline bound

SM: V7A

8cvm

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Cutibacterium acnes 50S ribosomal subunit with P-site tRNA and Sarecycline bound in the local refined map

SM: V7A

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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

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

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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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