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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2012-04-03 14:10:34 UTC

Update Date

2020-11-09 23:19:12 UTC

HMDB ID

HMDB0013695

Secondary Accession Numbers

HMDB13695

Metabolite Identification

Common Name

Urolithin A

Description

Urolithin A belongs to the class of organic compounds known as coumarins and derivatives. These are polycyclic aromatic compounds containing a 1-benzopyran moiety with a ketone group at the C2 carbon atom (1-benzopyran-2-one). Based on a literature review a significant number of articles have been published on Urolithin A.

Structure

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

  Mrv1652303102016532D          

 17 19  0  0  0  0            999 V2000
   -1.0326   -0.1759    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2076   -0.1759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2049    0.5386    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0299    0.5386    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4423   -0.1759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0299   -0.8904    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2049   -0.8904    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2674   -0.1759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6799    0.5386    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5049    0.5386    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9174   -0.1759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7424   -0.1759    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5049   -0.8904    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6799   -0.8904    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2674    1.2531    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6799    1.9675    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4423    1.2531    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  2  7  1  0  0  0  0
  5  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 11 13  1  0  0  0  0
 13 14  2  0  0  0  0
  8 14  1  0  0  0  0
  9 15  1  0  0  0  0
 15 16  2  0  0  0  0
 15 17  1  0  0  0  0
  4 17  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0013695

> <DATABASE_NAME>
hmdb

> <SMILES>
OC1=CC2=C(C=C1)C1=C(C=C(O)C=C1)C(=O)O2

> <INCHI_IDENTIFIER>
InChI=1S/C13H8O4/c14-7-1-3-9-10-4-2-8(15)6-12(10)17-13(16)11(9)5-7/h1-6,14-15H

> <INCHI_KEY>
RIUPLDUFZCXCHM-UHFFFAOYSA-N

> <FORMULA>
C13H8O4

> <MOLECULAR_WEIGHT>
228.2002

> <EXACT_MASS>
228.042258744

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
25

> <JCHEM_AVERAGE_POLARIZABILITY>
22.258403045305855

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
3,8-dihydroxy-6H-benzo[c]chromen-6-one

> <ALOGPS_LOGP>
2.16

> <JCHEM_LOGP>
2.318196798

> <ALOGPS_LOGS>
-2.94

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
7.9637712310585735

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.213762400702427

> <JCHEM_PKA_STRONGEST_BASIC>
-7.061837521358001

> <JCHEM_POLAR_SURFACE_AREA>
66.76

> <JCHEM_REFRACTIVITY>
60.90090000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.63e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3,8-dihydroxybenzo[c]chromen-6-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 10-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-MAR-20         0                                  
HETATM    1  O   UNK     0      -1.928  -0.328   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -0.388  -0.328   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.382   1.005   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.922   1.005   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.692  -0.328   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.922  -1.662   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.382  -1.662   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.232  -0.328   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.002   1.005   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.542   1.005   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       7.312  -0.328   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       8.852  -0.328   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       6.542  -1.662   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.002  -1.662   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.232   2.339   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       5.002   3.673   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       2.692   2.339   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   17                                                  
CONECT    5    4    6    8                                                  
CONECT    6    5    7                                                       
CONECT    7    6    2                                                       
CONECT    8    5    9   14                                                  
CONECT    9    8   10   15                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14   13    8                                                       
CONECT   15    9   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15    4                                                       
MASTER        0    0    0    0    0    0    0    0   17    0   38    0
END

View in JSmol View Stereo Labels

Synonyms

Value	Source
3,8-Dihydroxy-6H-dibenzo(b,D)pyran-6-one	HMDB
3,8-dihydroxy-6H-benzo[c]chromen-6-one	HMDB
3,8-dihydroxy-urolithin	HMDB

Chemical Formula

C₁₃H₈O₄

Average Molecular Weight

228.2002

Monoisotopic Molecular Weight

228.042258744

IUPAC Name

3,8-dihydroxy-6H-benzo[c]chromen-6-one

Traditional Name

3,8-dihydroxybenzo[c]chromen-6-one

CAS Registry Number

1143-70-0

SMILES

OC1=CC2=C(C=C1)C1=C(C=C(O)C=C1)C(=O)O2

InChI Identifier

InChI=1S/C13H8O4/c14-7-1-3-9-10-4-2-8(15)6-12(10)17-13(16)11(9)5-7/h1-6,14-15H

InChI Key

RIUPLDUFZCXCHM-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as coumarins and derivatives. These are polycyclic aromatic compounds containing a 1-benzopyran moiety with a ketone group at the C2 carbon atom (1-benzopyran-2-one).

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Coumarins and derivatives

Sub Class

Not Available

Direct Parent

Coumarins and derivatives

Alternative Parents

Substituents

Coumarin
Isocoumarin
Benzopyran
1-benzopyran
2-benzopyran
1-hydroxy-2-unsubstituted benzenoid
Pyranone
Pyran
Benzenoid
Heteroaromatic compound
Lactone
Oxacycle
Organoheterocyclic compound
Organooxygen compound
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 32966057)

Cellular substructure

Membrane (HMDB: HMDB0013695)
Cell membrane (HMDB: HMDB0013695)

Excreta

Biofluid or Excreta

Urine (PMID: 16988113)
Feces (PMID: 26848182)

Source

Exogenous

Exogenous (HMDB: HMDB0013695)

Food

Nut

Nuts (HMDB: HMDB0013695)

Beverage

Alcoholic beverage

Red wine (HMDB: HMDB0013695)

Fruit

Berries (HMDB: HMDB0013695)

Endogenous

Endogenous (HMDB: HMDB0013695)

Plant

Plant (HMDB: HMDB0013695)

Process

Not Available

Role

Not Available

Physical Properties

State

Solid

Experimental Molecular 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

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.26 g/L	ALOGPS
logP	2.16	ALOGPS
logP	2.32	ChemAxon
logS	-2.9	ALOGPS
pKa (Strongest Acidic)	7.21	ChemAxon
pKa (Strongest Basic)	-7.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	66.76 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	60.9 m³·mol⁻¹	ChemAxon
Polarizability	22.26 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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]+	150.865	31661259
DarkChem	[M-H]-	150.817	31661259
DeepCCS	[M+H]+	153.15	30932474
DeepCCS	[M-H]-	150.792	30932474
DeepCCS	[M-2H]-	183.811	30932474
DeepCCS	[M+Na]+	159.244	30932474
AllCCS	[M+H]+	149.2	32859911
AllCCS	[M+H-H2O]+	145.0	32859911
AllCCS	[M+NH4]+	153.1	32859911
AllCCS	[M+Na]+	154.2	32859911
AllCCS	[M-H]-	150.5	32859911
AllCCS	[M+Na-2H]-	149.8	32859911
AllCCS	[M+HCOO]-	149.1	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Urolithin A	OC1=CC2=C(C=C1)C1=C(C=C(O)C=C1)C(=O)O2	3701.7	Standard polar	33892256
Urolithin A	OC1=CC2=C(C=C1)C1=C(C=C(O)C=C1)C(=O)O2	2408.0	Standard non polar	33892256
Urolithin A	OC1=CC2=C(C=C1)C1=C(C=C(O)C=C1)C(=O)O2	2706.5	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Urolithin A,1TMS,isomer #1	C[Si](C)(C)OC1=CC=C2C(=C1)OC(=O)C1=CC(O)=CC=C12	2647.1	Semi standard non polar	33892256
Urolithin A,1TMS,isomer #2	C[Si](C)(C)OC1=CC=C2C(=C1)C(=O)OC1=CC(O)=CC=C12	2655.5	Semi standard non polar	33892256
Urolithin A,2TMS,isomer #1	C[Si](C)(C)OC1=CC=C2C(=C1)OC(=O)C1=CC(O[Si](C)(C)C)=CC=C12	2769.5	Semi standard non polar	33892256
Urolithin A,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1=CC=C2C(=C1)OC(=O)C1=CC(O)=CC=C12	2858.0	Semi standard non polar	33892256
Urolithin A,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC1=CC=C2C(=C1)C(=O)OC1=CC(O)=CC=C12	2870.1	Semi standard non polar	33892256
Urolithin A,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1=CC=C2C(=C1)OC(=O)C1=CC(O[Si](C)(C)C(C)(C)C)=CC=C12	3202.5	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Urolithin A GC-MS (Non-derivatized) - 70eV, Positive	splash10-0fai-0980000000-794e7711dd60a731dd65	2017-07-27	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Urolithin A GC-MS (2 TMS) - 70eV, Positive	splash10-00di-5169000000-c16bd42945ba6a7b5723	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Urolithin A 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 - Urolithin A 10V, Positive-QTOF	splash10-004i-0090000000-1cfecfbcd459b8f927aa	2015-04-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Urolithin A 20V, Positive-QTOF	splash10-004i-0190000000-1fb96de3cadd65f74445	2015-04-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Urolithin A 40V, Positive-QTOF	splash10-052s-0910000000-f66d25e749ba2d69c3ab	2015-04-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Urolithin A 10V, Negative-QTOF	splash10-004i-0190000000-637b053a07946e3af236	2015-04-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Urolithin A 20V, Negative-QTOF	splash10-004i-0390000000-e87f1d5246d5b9e763da	2015-04-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Urolithin A 40V, Negative-QTOF	splash10-001i-0910000000-11d70b77e5008c99715d	2015-04-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Urolithin A 10V, Positive-QTOF	splash10-004i-0090000000-02cbe499adea44a39627	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Urolithin A 20V, Positive-QTOF	splash10-004i-0090000000-ca73ea1f706aac82d0ed	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Urolithin A 40V, Positive-QTOF	splash10-0kmr-0920000000-0d73ab6b0c4deb404c6d	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Urolithin A 10V, Negative-QTOF	splash10-004i-0090000000-d8e725b6742766a16bb5	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Urolithin A 20V, Negative-QTOF	splash10-004i-0090000000-d8e725b6742766a16bb5	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Urolithin A 40V, Negative-QTOF	splash10-007k-0900000000-f4e034446778df31e9b7	2021-09-24	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Membrane (predicted from logP)

Biospecimen Locations

Blood
Feces
Urine

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	32966057	details
Urine	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	32966057	details
Urine	Expected but not Quantified	Not Quantified	Not Available	Not Available	Consuming polyphenols described by Phenol-Explorer entry 1038	16988113	details
Urine	Expected but not Quantified	Not Quantified	Not Available	Not Available	Consuming polyphenols described by Phenol-Explorer entry 1038	17090147	details

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Inflammatory bowel disease	26848182	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Metastatic melanoma	28923537	details

Associated Disorders and Diseases

Disease References

Inflammatory bowel disease
Lee T, Clavel T, Smirnov K, Schmidt A, Lagkouvardos I, Walker A, Lucio M, Michalke B, Schmitt-Kopplin P, Fedorak R, Haller D: Oral versus intravenous iron replacement therapy distinctly alters the gut microbiota and metabolome in patients with IBD. Gut. 2017 May;66(5):863-871. doi: 10.1136/gutjnl-2015-309940. Epub 2016 Feb 4. [PubMed:26848182 ]
Metastatic melanoma
Frankel AE, Coughlin LA, Kim J, Froehlich TW, Xie Y, Frenkel EP, Koh AY: Metagenomic Shotgun Sequencing and Unbiased Metabolomic Profiling Identify Specific Human Gut Microbiota and Metabolites Associated with Immune Checkpoint Therapy Efficacy in Melanoma Patients. Neoplasia. 2017 Oct;19(10):848-855. doi: 10.1016/j.neo.2017.08.004. Epub 2017 Sep 15. [PubMed:28923537 ]

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB029999

KNApSAcK ID

C00053884

Chemspider ID

4589709

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Urolithin A

METLIN ID

Not Available

PubChem Compound

5488186

PDB ID

Not Available

ChEBI ID

1280327

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

Not Available

Enzymes

Enzyme Details

1. UDP-glucuronosyltransferase 1-1

General function:: Involved in transferase activity, transferring hexosyl groups
Specific function:: UDPGT is of major importance in the conjugation and subsequent elimination of potentially toxic xenobiotics and endogenous compounds. This isoform glucuronidates bilirubin IX-alpha to form both the IX-alpha-C8 and IX-alpha-C12 monoconjugates and diconjugate. Is also able to catalyze the glucuronidation of 17beta-estradiol, 17alpha-ethinylestradiol, 1-hydroxypyrene, 4-methylumbelliferone, 1-naphthol, paranitrophenol, scopoletin, and umbelliferone.
Gene Name:: UGT1A1
Uniprot ID:: P22309
Molecular weight:: 59590.91

Reactions

Urolithin A → 3,4,5-trihydroxy-6-({3-hydroxy-6-oxo-6H-benzo[c]chromen-8-yl}oxy)oxane-2-carboxylic acid	details
Urolithin A → Urolithin A-3-O-glucuronide	details

Showing metabocard for Urolithin A (HMDB0013695)

MOL for HMDB0013695 (Urolithin A)

3D MOL for HMDB0013695 (Urolithin A)

3D SDF for HMDB0013695 (Urolithin A)

3D-SDF for HMDB0013695 (Urolithin A)

PDB for HMDB0013695 (Urolithin A)

3D PDB for HMDB0013695 (Urolithin A)

SMILES for HMDB0013695 (Urolithin A)

INCHI for HMDB0013695 (Urolithin A)

Structure for HMDB0013695 (Urolithin A)

3D Structure for HMDB0013695 (Urolithin A)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

Enzymes

Reactions