NP-MRD: Showing NP-Card for 6-Dehydrotestosterone glucuronide (NP0090892)

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Record Information

Version

2.0

Created at

2022-05-11 18:25:15 UTC

Updated at

2022-05-11 18:25:15 UTC

NP-MRD ID

NP0090892

Secondary Accession Numbers

None

Natural Product Identification

Common Name

6-Dehydrotestosterone glucuronide

Description

Thymine, also known as 5-methyluracil, belongs to the class of organic compounds known as hydroxypyrimidines. These are organic compounds containing a hydroxyl group attached to a pyrimidine ring. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions. Thymine is an extremely weak basic (essentially neutral) compound (based on its pKa). Thymine exists in all living species, ranging from bacteria to humans. Within humans, thymine participates in a number of enzymatic reactions. In particular, thymine and deoxyribose 1-phosphate can be biosynthesized from thymidine through its interaction with the enzyme thymidine phosphorylase. In addition, thymine can be converted into dihydrothymine through its interaction with the enzyme dihydropyrimidine dehydrogenase [nadp(+)]. In humans, thymine is involved in the metabolic disorder called the beta-ureidopropionase deficiency pathway. Outside of the human body, Thymine has been detected, but not quantified in, several different foods, such as cupuaçus, welsh onions, wild leeks, jujubes, and black raspberries. This could make thymine a potential biomarker for the consumption of these foods. Thymine is a potentially toxic compound. A pyrimidine nucleobase that is uracil in which the hydrogen at position 5 is replaced by a methyl group. 6-Dehydrotestosterone glucuronide was first documented in 2000 (PMID: 10877825). Thymine, with regard to humans, has been found to be associated with several diseases such as colorectal cancer, thymidine treatment, and periodontal probing depth; thymine has also been linked to several inborn metabolic disorders including dihydropyrimidine dehydrogenase deficiency and beta-ureidopropionase deficiency (PMID: 12926795) (PMID: 23438684) (PMID: 29565828) (PMID: 23237383).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv0541 02241200512D          

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M  END

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  Mrv0541 02241200512D          

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 17 22  1  0  0  0  0
 17 23  1  1  0  0  0
 20 24  2  0  0  0  0
 21 24  1  0  0  0  0
 21 26  2  0  0  0  0
 22 25  1  0  0  0  0
 25 28  1  0  0  0  0
 26 28  1  0  0  0  0
 27 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 32  1  0  0  0  0
 31 32  1  0  0  0  0
 31 33  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0090892

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@@]12CC[C@H](O[C@@H]3O[C@@H]([C@@H](O)[C@H](O)[C@H]3O)C(O)=O)[C@@]1(C)CC[C@@]1([H])[C@@]2([H])C=CC2=CC(=O)CC[C@]12C

> <INCHI_IDENTIFIER>
InChI=1S/C25H34O8/c1-24-9-7-13(26)11-12(24)3-4-14-15-5-6-17(25(15,2)10-8-16(14)24)32-23-20(29)18(27)19(28)21(33-23)22(30)31/h3-4,11,14-21,23,27-29H,5-10H2,1-2H3,(H,30,31)/t14-,15-,16-,17-,18-,19-,20+,21-,23+,24-,25-/m0/s1

> <INCHI_KEY>
GCIVSXAHMONYLO-HMAFJQTKSA-N

> <FORMULA>
C25H34O8

> <MOLECULAR_WEIGHT>
462.5327

> <EXACT_MASS>
462.225368064

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_AVERAGE_POLARIZABILITY>
48.80357772138917

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2S,3S,4S,5R,6R)-6-{[(1S,2R,10R,11S,14S,15S)-2,15-dimethyl-5-oxotetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadeca-6,8-dien-14-yl]oxy}-3,4,5-trihydroxyoxane-2-carboxylic acid

> <ALOGPS_LOGP>
1.87

> <JCHEM_LOGP>
1.5529405333333335

> <ALOGPS_LOGS>
-3.14

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.227590429886526

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.6580352007224812

> <JCHEM_PKA_STRONGEST_BASIC>
-3.686499496642874

> <JCHEM_POLAR_SURFACE_AREA>
133.52

> <JCHEM_REFRACTIVITY>
117.82709999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.32e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3S,4S,5R,6R)-6-{[(1S,2R,10R,11S,14S,15S)-2,15-dimethyl-5-oxotetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadeca-6,8-dien-14-yl]oxy}-3,4,5-trihydroxyoxane-2-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  O   UNK     0      34.290  -9.744   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      36.825 -10.573   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      24.049 -16.377   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      35.247  -6.816   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      38.260  -6.181   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      40.317  -8.474   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      40.867 -11.084   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      38.882 -12.865   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      32.354 -11.677   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      32.354 -13.217   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      31.021 -13.987   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      29.687 -13.217   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      33.811 -11.208   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      31.021 -10.907   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      33.811 -13.686   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      29.687 -11.677   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      28.285 -13.998   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      34.710 -12.447   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      32.354 -10.137   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      31.045 -15.591   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      28.273 -15.602   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      26.858 -13.129   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      28.297 -12.458   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      29.662 -16.404   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      25.398 -13.942   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      26.833 -16.448   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      35.797  -9.426   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      25.386 -15.613   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      36.275  -7.963   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      37.782  -7.645   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      38.332 -10.255   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      38.810  -8.791   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      39.361 -11.401   0.000  0.00  0.00           C+0
HETATM   34  H   UNK     0      32.493 -14.519   0.000  0.00  0.00           H+0
HETATM   35  H   UNK     0      31.107 -12.477   0.000  0.00  0.00           H+0
HETATM   36  H   UNK     0      29.691 -14.975   0.000  0.00  0.00           H+0
CONECT    1   13   27                                                       
CONECT    2   27   31                                                       
CONECT    3   28                                                            
CONECT    4   29                                                            
CONECT    5   30                                                            
CONECT    6   32                                                            
CONECT    7   33                                                            
CONECT    8   33                                                            
CONECT    9   10   13   14   19                                             
CONECT   10    9   11   15   34                                             
CONECT   11   10   12   20   35                                             
CONECT   12   11   16   17   36                                             
CONECT   13    1    9   18                                                  
CONECT   14    9   16                                                       
CONECT   15   10   18                                                       
CONECT   16   12   14                                                       
CONECT   17   12   21   22   23                                             
CONECT   18   13   15                                                       
CONECT   19    9                                                            
CONECT   20   11   24                                                       
CONECT   21   17   24   26                                                  
CONECT   22   17   25                                                       
CONECT   23   17                                                            
CONECT   24   20   21                                                       
CONECT   25   22   28                                                       
CONECT   26   21   28                                                       
CONECT   27    1    2   29                                                  
CONECT   28    3   25   26                                                  
CONECT   29    4   27   30                                                  
CONECT   30    5   29   32                                                  
CONECT   31    2   32   33                                                  
CONECT   32    6   30   31                                                  
CONECT   33    7    8   31                                                  
CONECT   34   10                                                            
CONECT   35   11                                                            
CONECT   36   12                                                            
MASTER        0    0    0    0    0    0    0    0   36    0   80    0
END

View in JSmol

Synonyms

Value	Source
2,4-Dihydroxy-5-methylpyrimidine	ChEBI
5-Methyl-2,4(1H,3H)-pyrimidinedione	ChEBI
5-Methylpyrimidine-2,4(1H,3H)-dione	ChEBI
5-Methyluracil	ChEBI
T	ChEBI
Thy	ChEBI
Thymin	ChEBI
4-Hydroxy-5-methylpyrimidin-2(1H)-one	HMDB
5-Methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione	HMDB
5-Methyl-2,4-dihydroxypyrimidine	HMDB
5-Methylpyrimidine-2,4-dione	HMDB
5 Methyluracil	HMDB
6,7-Didehydrotestosterone O-glucuronide	ChEBI
6-Dehydrotestosterone O-glucuronide	ChEBI
3-Oxoandrosta-4,6-dien-17beta-yl beta-D-glucopyranosiduronic acid	HMDB
3-Oxoandrosta-4,6-dien-17beta-yl beta-delta-glucopyranosiduronic acid	HMDB
6-Dehydrotestosterone 17-glucosiduronic acid	HMDB
6-Dehydrotestosterone 17-glucosiduronate	Generator

Chemical Formula

C₂₅H₃₄O₈

Average Mass

462.5327 Da

Monoisotopic Mass

462.22537 Da

IUPAC Name

(2S,3S,4S,5R,6R)-6-{[(1S,2R,10R,11S,14S,15S)-2,15-dimethyl-5-oxotetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadeca-6,8-dien-14-yl]oxy}-3,4,5-trihydroxyoxane-2-carboxylic acid

Traditional Name

(2S,3S,4S,5R,6R)-6-{[(1S,2R,10R,11S,14S,15S)-2,15-dimethyl-5-oxotetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadeca-6,8-dien-14-yl]oxy}-3,4,5-trihydroxyoxane-2-carboxylic acid

CAS Registry Number

Not Available

SMILES

[H][C@@]12CC[C@H](O[C@@H]3O[C@@H]([C@@H](O)[C@H](O)[C@H]3O)C(O)=O)[C@@]1(C)CC[C@@]1([H])[C@@]2([H])C=CC2=CC(=O)CC[C@]12C

InChI Identifier

InChI=1S/C25H34O8/c1-24-9-7-13(26)11-12(24)3-4-14-15-5-6-17(25(15,2)10-8-16(14)24)32-23-20(29)18(27)19(28)21(33-23)22(30)31/h3-4,11,14-21,23,27-29H,5-10H2,1-2H3,(H,30,31)/t14-,15-,16-,17-,18-,19-,20+,21-,23+,24-,25-/m0/s1

InChI Key

GCIVSXAHMONYLO-HMAFJQTKSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Anas platyrhynchos	FooDB	FooDB
Anatidae	FooDB	FooDB
Anser anser	FooDB	FooDB
Bison bison	FooDB	FooDB
Bos taurus	FooDB	FooDB
Bos taurus X Bison bison	FooDB	FooDB
Bubalus bubalis	FooDB	FooDB
Capra aegagrus hircus	FooDB	FooDB
Cervidae	FooDB	FooDB
Cervus canadensis	FooDB	FooDB
Columba	FooDB	FooDB
Columbidae	FooDB	FooDB
Dromaius novaehollandiae	FooDB	FooDB
Equus caballus	FooDB	FooDB
Gallus gallus	FooDB	FooDB
Lagopus muta	FooDB	FooDB
Leporidae	FooDB	FooDB
Lepus timidus	FooDB	FooDB
Melanitta fusca	FooDB	FooDB
Meleagris gallopavo	FooDB	FooDB
Numida meleagris	FooDB	FooDB
Odocoileus	FooDB	FooDB
Oryctolagus	FooDB	FooDB
Ovis aries	FooDB	FooDB
Phasianidae	FooDB	FooDB
Phasianus colchicus	FooDB	FooDB
Struthio camelus	FooDB	FooDB
Sus scrofa	FooDB	FooDB
Sus scrofa domestica	FooDB	FooDB

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as hydroxypyrimidines. These are organic compounds containing a hydroxyl group attached to a pyrimidine ring. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Diazines

Sub Class

Pyrimidines and pyrimidine derivatives

Direct Parent

Hydroxypyrimidines

Alternative Parents

Substituents

Hydroxypyrimidine
Heteroaromatic compound
Azacycle
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

pyrimidone (CHEBI:17821 )
pyrimidine nucleobase (CHEBI:17821 )
pyrimidines (C00178 )
a pyrimidine-related compound (THYMINE )
a pyrimidine base (THYMINE )

Physical Properties

State

Not Available

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	1.87	ALOGPS
logP	1.55	ChemAxon
logS	-3.1	ALOGPS
pKa (Strongest Acidic)	3.66	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	133.52 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	117.83 m³·mol⁻¹	ChemAxon
Polarizability	48.8 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0000262

DrugBank ID

DB03462

Phenol Explorer Compound ID

Not Available

FoodDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

Not Available

BiGG ID

Wikipedia Link

METLIN ID

PubChem Compound

PDB ID

Not Available

ChEBI ID

17821

Good Scents ID

Not Available

References

General References

Goukassian D, Gad F, Yaar M, Eller MS, Nehal US, Gilchrest BA: Mechanisms and implications of the age-associated decrease in DNA repair capacity. FASEB J. 2000 Jul;14(10):1325-34. [PubMed:10877825 ]
Wassberg C, Backvall H, Diffey B, Ponten F, Berne B: Enhanced epidermal ultraviolet responses in chronically sun-exposed skin are dependent on previous sun exposure. Acta Derm Venereol. 2003;83(4):254-61. [PubMed:12926795 ]
Melzer N, Wittenburg D, Hartwig S, Jakubowski S, Kesting U, Willmitzer L, Lisec J, Reinsch N, Repsilber D: Investigating associations between milk metabolite profiles and milk traits of Holstein cows. J Dairy Sci. 2013 Mar;96(3):1521-34. doi: 10.3168/jds.2012-5743. [PubMed:23438684 ]
Pan L, Yu J, Mi Z, Mo L, Jin H, Yao C, Ren D, Menghe B: A Metabolomics Approach Uncovers Differences between Traditional and Commercial Dairy Products in Buryatia (Russian Federation). Molecules. 2018 Mar 22;23(4). pii: molecules23040735. doi: 10.3390/molecules23040735. [PubMed:29565828 ]
Shetlar MD, Basus VJ: The photochemistry of thymine in frozen aqueous solution: trimeric and minor dimeric products. Photochem Photobiol. 2013 May-Jun;89(3):631-9. doi: 10.1111/php.12033. Epub 2013 Jan 29. [PubMed:23237383 ]

Showing NP-Card for 6-Dehydrotestosterone glucuronide (NP0090892)

MOL for NP0090892 (6-Dehydrotestosterone glucuronide)

3D MOL for NP0090892 (6-Dehydrotestosterone glucuronide)

3D SDF for NP0090892 (6-Dehydrotestosterone glucuronide)

3D-SDF for NP0090892 (6-Dehydrotestosterone glucuronide)

PDB for NP0090892 (6-Dehydrotestosterone glucuronide)

3D PDB for NP0090892 (6-Dehydrotestosterone glucuronide)

SMILES for NP0090892 (6-Dehydrotestosterone glucuronide)

INCHI for NP0090892 (6-Dehydrotestosterone glucuronide)

Structure for NP0090892 (6-Dehydrotestosterone glucuronide)

3D Structure for NP0090892 (6-Dehydrotestosterone glucuronide)