Bovine Metabolome Database: Showing metabocard for Pseudouridine (BMDB0000767)

Identification Taxonomy Physical properties Pathways Spectra Concentrations Links References enzymes (3) Show 3 proteins XML

Record Information

Version

1.0

Creation Date

2016-09-30 22:36:17 UTC

Update Date

2020-06-04 20:46:21 UTC

BMDB ID

BMDB0000767

Secondary Accession Numbers

BMDB00767

Metabolite Identification

Common Name

Pseudouridine

Description

Beta-Pseudouridine, 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. Beta-Pseudouridine is possibly soluble (in water) and an extremely weak basic (essentially neutral) compound (based on its pKa). Beta-Pseudouridine exists in all living species, ranging from bacteria to humans.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
(1S)-1,4-Anhydro-1-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-D-ribitol	ChEBI
5-(beta-D-Ribofuranosyl)uracil	ChEBI
beta-Pseudouridine	ChEBI
p	ChEBI
Psi-uridine	ChEBI
5-(b-D-Ribofuranosyl)uracil	Generator
5-(Β-D-ribofuranosyl)uracil	Generator
b-Pseudouridine	Generator
Β-pseudouridine	Generator
5-(b-delta-Ribofuranosyl)uracil	HMDB
5-b-D-Ribofuranosyl-uracil	HMDB
5-beta-delta-Ribofuranosyl-uracil	HMDB
5-Ribosyluracil	HMDB
b-D-Pseudouridine	HMDB
beta-delta-Pseudouridine	HMDB
Pseudouridine C	HMDB
Y-uridine	HMDB
5-beta-D-Ribofuranosyl-2,4(1H,3H)-pyrimidinedione	HMDB
5-Β-D-ribofuranosyl-2,4(1H,3H)-pyrimidinedione	HMDB
beta-D-Pseudouridine	HMDB
Β-D-pseudouridine	HMDB
Ψ-uridine	HMDB
Pseudouridine	HMDB

Chemical Formula

C₉H₁₂N₂O₆

Average Molecular Weight

244.2014

Monoisotopic Molecular Weight

244.069536126

IUPAC Name

5-[(2S,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2,3,4-tetrahydropyrimidine-2,4-dione

Traditional Name

β-pseudouridine

CAS Registry Number

1445-07-4

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 Key

PTJWIQPHWPFNBW-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.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Nucleoside and nucleotide analogues

Sub Class

Not Available

Direct Parent

Nucleoside 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 Framework

Aromatic heteromonocyclic compounds

External Descriptors

pseudouridines (CHEBI:17802 )

Ontology

Status

Detected and Quantified

Origin

Endogenous

Biofunction

Not Available

Application

Not Available

Cellular locations

Cytoplasm

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	-2	ALOGPS
logP	-3.1	ChemAxon
logS	-0.58	ALOGPS
pKa (Strongest Acidic)	8.66	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	128.12 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	52.44 m³·mol⁻¹	ChemAxon
Polarizability	21.79 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Spectrum Type	Description	Splash Key
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0unc-7930000000-a1e7f343c88a63ac1976	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positive	splash10-0fi0-3494100000-8d726ed412554c1f92f0	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_5) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_4) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_5) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_6) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_7) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_8) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_9) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_10) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_4) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_5) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_6) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_7) - 70eV, Positive	Not Available	View in JSpectraViewer
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-IT , negative	splash10-0udi-0900000000-6ade42aaa885371e176c	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF 10V, positive	splash10-0a4i-0190000000-129f123affa0ecbf7a59	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF 20V, positive	splash10-052f-0910000000-302fbdef606070bd5a67	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF 40V, positive	splash10-001i-9300000000-11f5761be16d1b061df5	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 30V, Negative	splash10-0006-9600000000-7585746143c62ab3f832	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9100000000-010da2c57a936868eecc	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 40V, Positive	splash10-0kai-9200000000-12f986238bdf05dc39b9	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 30V, Positive	splash10-001i-9400000000-b6dbdfa2d4643fc13e70	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 10V, Positive	splash10-0a4i-0190000000-129f123affa0ecbf7a59	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 20V, Positive	splash10-052f-0910000000-302fbdef606070bd5a67	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 0V, Positive	splash10-0bta-0890000000-2b3810ae2bbe68268b17	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 40V, Positive	splash10-001i-9300000000-7e64dc8404ac65411358	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 0V, Positive	splash10-052b-0290000000-7cf7d5be6f7a84299cab	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 10V, Positive	splash10-0a4i-0950000000-de2a45f204636756b9c4	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 30V, Positive	splash10-00l6-9000000000-b4060d47530bdf70d6cc	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 10V, Positive	splash10-0a4i-3920000000-15bb158a77906d0f87b5	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 20V, Negative	splash10-0udi-2900000000-600643d24abd3ba9b5f1	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 10V, Negative	splash10-0udi-0920000000-a73049fd7001db7f72d5	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 20V, Negative	splash10-0udi-0900000000-46e1b064445ad43a60fd	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0002-0490000000-226d044c24dd80a7c2ca	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0h0s-2980000000-add34ee37b95c102114d	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-06rm-5900000000-8d66d80928e84e9c93fd	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0006-9360000000-3bd8fcdd66c5d245778e	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0006-9210000000-f551740a13c90ff1d324	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9000000000-bf4e4234a47d8aa03828	View in MoNA
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, experimental)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer

Biological Properties

Cellular Locations

Cytoplasm

Biospecimen Locations

Liver
Milk
Placenta

Pathways

Not Available

Name	SMPDB/Pathwhiz	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Liver	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	PMID: 31867104	details
Milk	Detected and Quantified	3.8 uM	Not Specified	Not Specified	Normal	PMID: 6539345	details
Placenta	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details

Abnormal Concentrations

Not Available

External Links

HMDB ID

HMDB0000767

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Not Available

Wikipedia Link

Pseudouridine

METLIN ID

5734

PubChem Compound

15047

PDB ID

Not Available

ChEBI ID

17802

References

Synthesis Reference

anessian, Stephen; Machaalani, Roger. A highly stereo-controlled and efficient synthesis of a- and b-pseudouridines. Tetrahedron Letters (2003), 44(45), 8321-8323.

Material Safety Data Sheet (MSDS)

Not Available

General References

Tiemeyer W, Stohrer M, Giesecke D: Metabolites of nucleic acids in bovine milk. J Dairy Sci. 1984 Apr;67(4):723-8. doi: 10.3168/jds.S0022-0302(84)81361-2. [PubMed:6539345 ]

Enzymes

Enzyme Details

1. tRNA pseudouridine synthase

General function:: Translation, ribosomal structure and biogenesis
Specific function:: Not Available
Gene Name:: PUSL1
Uniprot ID:: A6QP68
Molecular weight:: 34022.0

Enzyme Details

2. Pseudouridylate synthase 7 homolog

General function:: Involved in pseudouridine synthase activity
Specific function:: Pseudouridylate synthase that catalyzes pseudouridylation of RNAs. Acts as a regulator of protein synthesis in embryonic stem cells by mediating pseudouridylation of RNA fragments derived from tRNAs (tRFs): pseudouridylated tRFs inhibit translation by targeting the translation initiation complex. Also catalyzes pseudouridylation of mRNAs: mediates pseudouridylation of mRNAs with the consensus sequence 5'-UGUAG-3'. In addition to mRNAs and tRNAs, binds other types of RNAs, such as snRNAs, Y RNAs and vault RNAs, suggesting that it can catalyze pseudouridylation of many RNA types.
Gene Name:: PUS7
Uniprot ID:: Q08DI8
Molecular weight:: 74594.0

Enzyme Details

3. tRNA pseudouridine(38/39) synthase

General function:: Translation, ribosomal structure and biogenesis
Specific function:: Formation of pseudouridine at position 39 in the anticodon stem and loop of transfer RNAs.
Gene Name:: PUS3
Uniprot ID:: Q3SX07
Molecular weight:: 55665.0

Showing metabocard for Pseudouridine (BMDB0000767)

Structure for BMDB0000767 (Pseudouridine)

Enzymes