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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 21:34:11 UTC

Update Date

2023-02-21 17:25:22 UTC

HMDB ID

HMDB0036431

Secondary Accession Numbers

HMDB36431

Metabolite Identification

Common Name

1,3,9-Trimethyluric acid

Description

1,3,9-Trimethyluric acid, also known as 1,3,9-trimethylate, belongs to the class of organic compounds known as xanthines. These are purine derivatives with a ketone group conjugated at carbons 2 and 6 of the purine moiety. 1,3,9-Trimethyluric acid has been detected, but not quantified in, a few different foods, such as arabica coffees (Coffea arabica), coffee and coffee products, and robusta coffees (Coffea canephora). This could make 1,3,9-trimethyluric acid a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on 1,3,9-Trimethyluric acid.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

  Mrv0541 02241217022D          

 15 16  0  0  0  0            999 V2000
   -1.7555   -0.0004    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9385   -0.2443    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3671    0.3264    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4492   -0.0004    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9385    0.7345    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7555    0.7345    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6125   -0.7345    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4288   -0.7345    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6939    2.1230    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4492    1.3881    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3671    1.1427    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5108   -1.4694    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7752   -1.0613    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0403   -1.3060    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1223   -2.1230    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  2 13  1  0  0  0  0
  3  4  2  0  0  0  0
  3 11  1  0  0  0  0
  4  5  1  0  0  0  0
  4  7  1  0  0  0  0
  5  6  1  0  0  0  0
  5 10  1  0  0  0  0
  7  8  1  0  0  0  0
  7 14  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0036431

> <DATABASE_NAME>
hmdb

> <SMILES>
CN1C(=O)NC2=C1N(C)C(=O)N(C)C2=O

> <INCHI_IDENTIFIER>
InChI=1S/C8H10N4O3/c1-10-5-4(9-7(10)14)6(13)12(3)8(15)11(5)2/h1-3H3,(H,9,14)

> <INCHI_KEY>
CWENCZHQIWXCCA-UHFFFAOYSA-N

> <FORMULA>
C8H10N4O3

> <MOLECULAR_WEIGHT>
210.19

> <EXACT_MASS>
210.075290206

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
19.75786885981796

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1,3,9-trimethyl-2,3,6,7,8,9-hexahydro-1H-purine-2,6,8-trione

> <ALOGPS_LOGP>
-0.46

> <JCHEM_LOGP>
-0.8731647386666664

> <ALOGPS_LOGS>
-0.86

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.778577822576182

> <JCHEM_PKA_STRONGEST_BASIC>
-5.633732262274788

> <JCHEM_POLAR_SURFACE_AREA>
72.96000000000001

> <JCHEM_REFRACTIVITY>
60.31869999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.90e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1,3,9-trimethyl-7H-purine-2,6,8-trione

> <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      -3.277  -0.001   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -1.752  -0.456   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.685   0.609   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.839  -0.001   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       1.752   1.371   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       3.277   1.371   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       1.143  -1.371   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       2.667  -1.371   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       1.295   3.963   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       0.839   2.591   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0      -0.685   2.133   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0      -2.820  -2.743   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0      -1.447  -1.981   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0      -0.075  -2.438   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       0.228  -3.963   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   13                                                  
CONECT    3    2    4   11                                                  
CONECT    4    3    5    7                                                  
CONECT    5    4    6   10                                                  
CONECT    6    5                                                            
CONECT    7    4    8   14                                                  
CONECT    8    7                                                            
CONECT    9   10                                                            
CONECT   10    5    9   11                                                  
CONECT   11    3   10                                                       
CONECT   12   13                                                            
CONECT   13    2   12   14                                                  
CONECT   14    7   13   15                                                  
CONECT   15   14                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   32    0
END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
1,3,9-Trimethylate	Generator
1,3,9-Trimethylic acid	Generator
1,3,9-Trimethyl-7,9-dihydro-1H-purine-2,6,8(3H)-trione	HMDB
7,9-dihydro-1,3,9-Trimethyl-1H-purine-2,6,8(3H)-trione	HMDB
8-Oxocaffeine	HMDB

Chemical Formula

C₈H₁₀N₄O₃

Average Molecular Weight

210.19

Monoisotopic Molecular Weight

210.075290206

IUPAC Name

1,3,9-trimethyl-2,3,6,7,8,9-hexahydro-1H-purine-2,6,8-trione

Traditional Name

1,3,9-trimethyl-7H-purine-2,6,8-trione

CAS Registry Number

7464-93-9

SMILES

CN1C(=O)NC2=C1N(C)C(=O)N(C)C2=O

InChI Identifier

InChI=1S/C8H10N4O3/c1-10-5-4(9-7(10)14)6(13)12(3)8(15)11(5)2/h1-3H3,(H,9,14)

InChI Key

CWENCZHQIWXCCA-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as xanthines. These are purine derivatives with a ketone group conjugated at carbons 2 and 6 of the purine moiety.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Imidazopyrimidines

Sub Class

Purines and purine derivatives

Direct Parent

Xanthines

Alternative Parents

Substituents

Xanthine
6-oxopurine
Purinone
Alkaloid or derivatives
Pyrimidone
N-substituted imidazole
Pyrimidine
Azole
Imidazole
Heteroaromatic compound
Vinylogous amide
Lactam
Urea
Azacycle
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organooxygen compound
Organonitrogen compound
Organic oxygen compound
Organic nitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Extracellular (HMDB: HMDB0036431)
Cytoplasm (HMDB: HMDB0036431)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0036431)

Source

Exogenous

Exogenous (HMDB: HMDB0036431)

Food

Food (HMDB: HMDB0036431)

Coffee and coffee product

Coffee

Arabica coffee (FooDB: FOOD00059)
Robusta coffee (FooDB: FOOD00060)

Coffee and coffee products (FooDB: FOOD00861)

Endogenous

Plant

Coffea (HMDB: HMDB0036431)

Process

Not Available

Role

Biological role

Nutrient (HMDB: HMDB0036431)

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	335 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	29 g/L	ALOGPS
logP	-0.46	ALOGPS
logP	-0.87	ChemAxon
logS	-0.86	ALOGPS
pKa (Strongest Acidic)	7.78	ChemAxon
pKa (Strongest Basic)	-5.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	72.96 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	60.32 m³·mol⁻¹	ChemAxon
Polarizability	19.76 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	146.113	31661259
DarkChem	[M-H]-	143.892	31661259
DeepCCS	[M+H]+	139.016	30932474
DeepCCS	[M-H]-	136.621	30932474
DeepCCS	[M-2H]-	170.773	30932474
DeepCCS	[M+Na]+	145.359	30932474
AllCCS	[M+H]+	143.6	32859911
AllCCS	[M+H-H2O]+	139.6	32859911
AllCCS	[M+NH4]+	147.3	32859911
AllCCS	[M+Na]+	148.4	32859911
AllCCS	[M-H]-	144.5	32859911
AllCCS	[M+Na-2H]-	144.8	32859911
AllCCS	[M+HCOO]-	145.2	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
1,3,9-Trimethyluric acid	CN1C(=O)NC2=C1N(C)C(=O)N(C)C2=O	2312.1	Standard polar	33892256
1,3,9-Trimethyluric acid	CN1C(=O)NC2=C1N(C)C(=O)N(C)C2=O	2194.2	Standard non polar	33892256
1,3,9-Trimethyluric acid	CN1C(=O)NC2=C1N(C)C(=O)N(C)C2=O	1984.8	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
1,3,9-Trimethyluric acid,1TMS,isomer #1	CN1C(=O)C2=C(N(C)C1=O)N(C)C(=O)N2[Si](C)(C)C	1952.7	Semi standard non polar	33892256
1,3,9-Trimethyluric acid,1TMS,isomer #1	CN1C(=O)C2=C(N(C)C1=O)N(C)C(=O)N2[Si](C)(C)C	2195.8	Standard non polar	33892256
1,3,9-Trimethyluric acid,1TBDMS,isomer #1	CN1C(=O)C2=C(N(C)C1=O)N(C)C(=O)N2[Si](C)(C)C(C)(C)C	2148.6	Semi standard non polar	33892256
1,3,9-Trimethyluric acid,1TBDMS,isomer #1	CN1C(=O)C2=C(N(C)C1=O)N(C)C(=O)N2[Si](C)(C)C(C)(C)C	2404.1	Standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 1,3,9-Trimethyluric acid GC-MS (Non-derivatized) - 70eV, Positive	splash10-0udj-2910000000-6282aab8072b7e149b80	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 1,3,9-Trimethyluric acid GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 1,3,9-Trimethyluric acid GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,3,9-Trimethyluric acid 10V, Negative-QTOF	splash10-0a4i-0190000000-30bafcc29f7f8f52e84c	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,3,9-Trimethyluric acid 20V, Negative-QTOF	splash10-0a4i-0390000000-16f3b19561d03e23d20b	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,3,9-Trimethyluric acid 40V, Negative-QTOF	splash10-05mo-4900000000-6ad4bacaedfffaa2f502	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,3,9-Trimethyluric acid 10V, Negative-QTOF	splash10-0a4i-0090000000-42027b355fe6a1bc1d06	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,3,9-Trimethyluric acid 20V, Negative-QTOF	splash10-0a4i-7690000000-d02498f7bb599d5feeda	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,3,9-Trimethyluric acid 40V, Negative-QTOF	splash10-0fdo-9800000000-7d1539e06616315f6a93	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,3,9-Trimethyluric acid 10V, Positive-QTOF	splash10-03di-0090000000-2502fd56810d56eea853	2016-08-02	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,3,9-Trimethyluric acid 20V, Positive-QTOF	splash10-0ik9-0790000000-8a65f129c8151d98a863	2016-08-02	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,3,9-Trimethyluric acid 40V, Positive-QTOF	splash10-0wb9-3900000000-2c1f0413f2c6b3dc3f13	2016-08-02	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,3,9-Trimethyluric acid 10V, Positive-QTOF	splash10-03di-0090000000-6081cca74a09f579f843	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,3,9-Trimethyluric acid 20V, Positive-QTOF	splash10-03di-0290000000-c55e377d0f3a2f58f18f	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,3,9-Trimethyluric acid 40V, Positive-QTOF	splash10-0092-9600000000-367fec34feb776dbef38	2021-09-22	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum

IR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)	2023-02-04	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)	2023-02-04	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)	2023-02-04	FELIX lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm
Extracellular

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB015318

KNApSAcK ID

Not Available

Chemspider ID

73977

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

81972

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

(). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .

Showing metabocard for 1,3,9-Trimethyluric acid (HMDB0036431)

MOL for HMDB0036431 (1,3,9-Trimethyluric acid)

3D MOL for HMDB0036431 (1,3,9-Trimethyluric acid)

3D SDF for HMDB0036431 (1,3,9-Trimethyluric acid)

3D-SDF for HMDB0036431 (1,3,9-Trimethyluric acid)

PDB for HMDB0036431 (1,3,9-Trimethyluric acid)

3D PDB for HMDB0036431 (1,3,9-Trimethyluric acid)

SMILES for HMDB0036431 (1,3,9-Trimethyluric acid)

INCHI for HMDB0036431 (1,3,9-Trimethyluric acid)

Structure for HMDB0036431 (1,3,9-Trimethyluric acid)

3D Structure for HMDB0036431 (1,3,9-Trimethyluric acid)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra