Showing Compound Card for Pseudouridine (CDB004864)

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Record Information
Version1.0
Created at2020-04-17 18:44:39 UTC
Updated at2020-12-07 19:11:08 UTC
CannabisDB IDCDB004864
Secondary Accession NumbersNot Available
Cannabis Compound Identification
Common NamePseudouridine
DescriptionPseudouridine, also known as p or 5-ribosyluracil, belongs to the class of organic compounds known as nucleoside and nucleotide analogues. These are analogues of nucleosides and nucleotides. These include phosphonated nucleosides, C-glycosylated nucleoside bases, analogues where the sugar unit is a pyranose, and carbocyclic nucleosides, among others. Pseudouridine is an extremely weak basic (essentially neutral) compound (based on its pKa). Pseudouridine exists in all living species, ranging from bacteria to humans. Outside of the human body, Pseudouridine is found, on average, in the highest concentration within milk (cow). Pseudouridine has also been detected, but not quantified in, several different foods, such as black raspberries, italian oregano, brassicas, pak choy, and ryes. This could make pseudouridine a potential biomarker for the consumption of these foods. Pseudouridine is expected to be in Cannabis as all living plants are known to produce and metabolize it.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
(1S)-1,4-Anhydro-1-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-D-ribitolChEBI
5-(beta-D-Ribofuranosyl)uracilChEBI
beta-PseudouridineChEBI
pChEBI
Psi-uridineChEBI
5-(b-D-Ribofuranosyl)uracilGenerator
5-(Β-D-ribofuranosyl)uracilGenerator
b-PseudouridineGenerator
Β-pseudouridineGenerator
5-(b-delta-Ribofuranosyl)uracilHMDB
5-b-D-Ribofuranosyl-uracilHMDB
5-beta-delta-Ribofuranosyl-uracilHMDB
5-RibosyluracilHMDB
b-D-PseudouridineHMDB
beta-delta-PseudouridineHMDB
Pseudouridine CHMDB
Y-uridineHMDB
5-beta-D-Ribofuranosyl-2,4(1H,3H)-pyrimidinedioneHMDB
5-Β-D-ribofuranosyl-2,4(1H,3H)-pyrimidinedioneHMDB
beta-D-PseudouridineHMDB
Β-D-pseudouridineHMDB
Ψ-uridineHMDB
PseudouridineHMDB
Chemical FormulaC9H12N2O6
Average Molecular Weight244.2
Monoisotopic Molecular Weight244.0695
IUPAC Name5-[(2S,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2,3,4-tetrahydropyrimidine-2,4-dione
Traditional Nameβ-pseudouridine
CAS Registry Number1445-07-4
SMILES
OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)C1=CNC(=O)NC1=O
InChI Identifier
InChI=1S/C9H12N2O6/c12-2-4-5(13)6(14)7(17-4)3-1-10-9(16)11-8(3)15/h1,4-7,12-14H,2H2,(H2,10,11,15,16)/t4-,5-,6-,7+/m1/s1
InChI KeyPTJWIQPHWPFNBW-GBNDHIKLSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as nucleoside and nucleotide analogues. These are analogues of nucleosides and nucleotides. These include phosphonated nucleosides, C-glycosylated nucleoside bases, analogues where the sugar unit is a pyranose, and carbocyclic nucleosides, among others.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassNucleoside and nucleotide analogues
Sub ClassNot Available
Direct ParentNucleoside and nucleotide analogues
Alternative Parents
Substituents
  • C-glycosyl compound
  • Glycosyl compound
  • Pentose monosaccharide
  • Pyrimidone
  • Hydropyrimidine
  • Monosaccharide
  • Pyrimidine
  • Heteroaromatic compound
  • Tetrahydrofuran
  • Vinylogous amide
  • Lactam
  • Secondary alcohol
  • Urea
  • Azacycle
  • Oxacycle
  • Ether
  • Dialkyl ether
  • Organoheterocyclic compound
  • Primary alcohol
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxide
  • Alcohol
  • Organopnictogen compound
  • Organic oxygen compound
  • Organic nitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effect

Health effect:

Disposition

Route of exposure:

Source:

Biological location:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
logPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-2ALOGPS
logP-3.1ChemAxon
logS-0.58ALOGPS
pKa (Strongest Acidic)8.66ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area128.12 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity52.44 m³·mol⁻¹ChemAxon
Polarizability21.79 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Spectra
EI-MS/GC-MS
TypeDescriptionSplash KeyView
Predicted GC-MSPseudouridine, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positivesplash10-0unc-7930000000-a1e7f343c88a63ac1976Spectrum
Predicted GC-MSPseudouridine, 3 TMS, Predicted GC-MS Spectrum - 70eV, Positivesplash10-0fi0-3494100000-8d726ed412554c1f92f0Spectrum
Predicted GC-MSPseudouridine, non-derivatized, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPseudouridine, non-derivatized, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPseudouridine, TMS_1_1, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPseudouridine, TMS_1_2, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPseudouridine, TMS_1_3, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPseudouridine, TMS_1_4, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPseudouridine, TMS_1_5, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPseudouridine, TMS_2_1, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPseudouridine, TMS_2_2, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPseudouridine, TMS_2_3, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPseudouridine, TMS_2_4, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPseudouridine, TMS_2_5, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPseudouridine, TMS_2_6, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPseudouridine, TMS_2_7, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPseudouridine, TMS_2_8, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPseudouridine, TMS_2_9, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPseudouridine, TMS_2_10, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPseudouridine, TMS_3_2, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPseudouridine, TMS_3_3, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPseudouridine, TMS_3_4, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPseudouridine, TMS_3_5, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPseudouridine, TMS_3_6, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPseudouridine, TMS_3_7, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
MS/MS
TypeDescriptionSplash KeyView
MS/MSLC-MS/MS Spectrum - LC-ESI-IT , negativesplash10-0udi-0900000000-6ade42aaa885371e176c2017-09-14View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF 10V, positivesplash10-0a4i-0190000000-129f123affa0ecbf7a592020-07-21View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF 20V, positivesplash10-052f-0910000000-302fbdef606070bd5a672020-07-21View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF 40V, positivesplash10-001i-9300000000-11f5761be16d1b061df52020-07-21View Spectrum
MS/MSLC-MS/MS Spectrum - 30V, Negativesplash10-0006-9600000000-7585746143c62ab3f8322021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 40V, Negativesplash10-0006-9100000000-010da2c57a936868eecc2021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 40V, Positivesplash10-0kai-9200000000-12f986238bdf05dc39b92021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 30V, Positivesplash10-001i-9400000000-b6dbdfa2d4643fc13e702021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-0a4i-0190000000-129f123affa0ecbf7a592021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 20V, Positivesplash10-052f-0910000000-302fbdef606070bd5a672021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 0V, Positivesplash10-0bta-0890000000-2b3810ae2bbe68268b172021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 40V, Positivesplash10-001i-9300000000-7e64dc8404ac654113582021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 0V, Positivesplash10-052b-0290000000-7cf7d5be6f7a84299cab2021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-0a4i-0950000000-de2a45f204636756b9c42021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 30V, Positivesplash10-00l6-9000000000-b4060d47530bdf70d6cc2021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-0a4i-3920000000-15bb158a77906d0f87b52021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 20V, Negativesplash10-0udi-2900000000-600643d24abd3ba9b5f12021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 10V, Negativesplash10-0udi-0920000000-a73049fd7001db7f72d52021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 20V, Negativesplash10-0udi-0900000000-46e1b064445ad43a60fd2021-09-20View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0002-0490000000-226d044c24dd80a7c2ca2015-09-15View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0h0s-2980000000-add34ee37b95c102114d2015-09-15View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-06rm-5900000000-8d66d80928e84e9c93fd2015-09-15View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0006-9360000000-3bd8fcdd66c5d245778e2015-09-15View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0006-9210000000-f551740a13c90ff1d3242015-09-15View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9000000000-bf4e4234a47d8aa038282015-09-15View Spectrum
NMRNot Available
Pathways
Pathways
Protein Targets
Enzymes
Protein NameGene NameLocusUniprot IDDetails
tRNA pseudouridine synthase A, mitochondrialPUS112q24.33Q9Y606 details
H/ACA ribonucleoprotein complex subunit 4DKC1O60832 details
Putative tRNA pseudouridine synthase Pus10PUS102p16.1Q3MIT2 details
tRNA pseudouridine synthase 3PUS311q24.2Q9BZE2 details
Pseudouridylate synthase 7 homologPUS77q22.3Q96PZ0 details
Pseudouridylate synthase 7 homolog-like proteinPUS7L12q12Q9H0K6 details
RNA pseudouridylate synthase domain-containing protein 1RPUSD116p13.3Q9UJJ7 details
RNA pseudouridylate synthase domain-containing protein 2RPUSD215q13.3Q8IZ73 details
RNA pseudouridylate synthase domain-containing protein 3RPUSD33p25.3Q6P087 details
RNA pseudouridylate synthase domain-containing protein 4RPUSD411q24.2Q96CM3 details
Probable tRNA pseudouridine synthase 1TRUB110q25.3Q8WWH5 details
Probable tRNA pseudouridine synthase 2TRUB29q34.11O95900 details
tRNA pseudouridine synthase-like 1PUSL11p36.33Q8N0Z8 details
Pseudouridine-5'-monophosphataseHDHD1Xp22.32Q08623 details
TransportersNot Available
Metal Bindings
Protein NameGene NameLocusUniprot IDDetails
Pseudouridine-5'-monophosphataseHDHD1Xp22.32Q08623 details
ReceptorsNot Available
Transcriptional FactorsNot Available
Concentrations Data
Not Available
HMDB IDHMDB0000767
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB031139
KNApSAcK IDC00001508
Chemspider ID14319
KEGG Compound IDC02067
BioCyc IDCPD-497
BiGG IDNot Available
Wikipedia LinkPseudouridine
METLIN ID5734
PubChem Compound15047
PDB IDNot Available
ChEBI ID17802
References
General ReferencesNot Available

Only showing the first 10 proteins. There are 15 proteins in total.

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Enzymes

Enzyme Details
1. tRNA pseudouridine synthase A, mitochondrial
General function:
Involved in RNA binding
Specific function:
Converts specific uridines to PSI in a number of tRNA substrates. Acts on positions 27/28 in the anticodon stem and also positions 34 and 36 in the anticodon of an intron containing tRNA. Involved in regulation of nuclear receptor activity possibly through pseudouridylation of SRA1 RNA
Gene Name:
PUS1
Uniprot ID:
Q9Y606
Molecular weight:
47469.7
Enzyme Details
2. H/ACA ribonucleoprotein complex subunit 4
General function:
Involved in RNA processing
Specific function:
Required for ribosome biogenesis and telomere maintenance. Probable catalytic subunit of H/ACA small nucleolar ribonucleoprotein (H/ACA snoRNP) complex, which catalyzes pseudouridylation of rRNA. This involves the isomerization of uridine such that the ribose is subsequently attached to C5, instead of the normal N1. Each rRNA can contain up to 100 pseudouridine ('psi') residues, which may serve to stabilize the conformation of rRNAs. Also required for correct processing or intranuclear trafficking of TERC, the RNA component of the telomerase reverse transcriptase (TERT) holoenzyme
Gene Name:
DKC1
Uniprot ID:
O60832
Molecular weight:
57673.7
Enzyme Details
3. Putative tRNA pseudouridine synthase Pus10
General function:
Involved in RNA binding
Specific function:
Pseudouridylate synthases catalyze pseudouridination of structural RNAs, including transfer, ribosomal, and splicing RNAs. PUS10 catalyzes the formation of the universal psi55 in the GC loop of transfer RNAs (Probable). Modulator of TRAIL-induced cell death via activation of procaspase 8 and BID cleavage. Required for the progression of the apoptotic signal through intrinsic mitochondrial cell death
Gene Name:
PUS10
Uniprot ID:
Q3MIT2
Molecular weight:
60243.7
Enzyme Details
4. tRNA pseudouridine synthase 3
General function:
Involved in RNA binding
Specific function:
Formation of pseudouridine at position 39 in the anticodon stem and loop of transfer RNAs
Gene Name:
PUS3
Uniprot ID:
Q9BZE2
Molecular weight:
55647.0
Enzyme Details
5. Pseudouridylate synthase 7 homolog
General function:
Involved in RNA binding
Specific function:
tRNA uridine = tRNA pseudouridine
Gene Name:
PUS7
Uniprot ID:
Q96PZ0
Molecular weight:
75034.9
Enzyme Details
6. Pseudouridylate synthase 7 homolog-like protein
General function:
Involved in RNA binding
Specific function:
tRNA uridine = tRNA pseudouridine
Gene Name:
PUS7L
Uniprot ID:
Q9H0K6
Molecular weight:
80699.9
Enzyme Details
7. RNA pseudouridylate synthase domain-containing protein 1
General function:
Involved in RNA binding
Specific function:
Not Available
Gene Name:
RPUSD1
Uniprot ID:
Q9UJJ7
Molecular weight:
34755.2
Enzyme Details
8. RNA pseudouridylate synthase domain-containing protein 2
General function:
Involved in RNA binding
Specific function:
Not Available
Gene Name:
RPUSD2
Uniprot ID:
Q8IZ73
Molecular weight:
61311.0
Enzyme Details
9. RNA pseudouridylate synthase domain-containing protein 3
General function:
Involved in RNA binding
Specific function:
Not Available
Gene Name:
RPUSD3
Uniprot ID:
Q6P087
Molecular weight:
38460.4
Enzyme Details
10. RNA pseudouridylate synthase domain-containing protein 4
General function:
Involved in RNA binding
Specific function:
Not Available
Gene Name:
RPUSD4
Uniprot ID:
Q96CM3
Molecular weight:
42204.9

Only showing the first 10 proteins. There are 15 proteins in total.

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