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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 21:10:12 UTC

Update Date

2022-03-07 02:54:47 UTC

HMDB ID

HMDB0036103

Secondary Accession Numbers

HMDB36103

Metabolite Identification

Common Name

Geranic acid

Description

Geranic acid, also known as geranate, belongs to the class of organic compounds known as acyclic monoterpenoids. These are monoterpenes that do not contain a cycle. Based on a literature review a small amount of articles have been published on Geranic acid.

Structure

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

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  C   UNK     0       3.744  -0.873   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.077  -0.103   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.077   1.437   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.411  -0.873   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.410  -0.103   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.076  -0.873   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.257  -0.103   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.591  -0.873   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.257   1.437   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       7.745  -0.103   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       9.078  -0.873   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       7.745   1.437   0.000  0.00  0.00           O+0
CONECT    1    2    5                                                       
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2   10                                                       
CONECT    5    1    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7                                                            
CONECT   10    4   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   22    0
END

COMPND    HMDB0036103
HETATM    1  C1  UNL     1      -2.582   0.177  -1.585  1.00  0.00           C  
HETATM    2  C2  UNL     1      -2.803  -0.100  -0.148  1.00  0.00           C  
HETATM    3  C3  UNL     1      -4.172   0.040   0.412  1.00  0.00           C  
HETATM    4  C4  UNL     1      -1.813  -0.467   0.649  1.00  0.00           C  
HETATM    5  C5  UNL     1      -0.405  -0.624   0.135  1.00  0.00           C  
HETATM    6  C6  UNL     1       0.447   0.336   0.910  1.00  0.00           C  
HETATM    7  C7  UNL     1       1.869   0.292   0.508  1.00  0.00           C  
HETATM    8  C8  UNL     1       2.817   1.200   1.205  1.00  0.00           C  
HETATM    9  C9  UNL     1       2.294  -0.511  -0.425  1.00  0.00           C  
HETATM   10  C10 UNL     1       3.684  -0.575  -0.838  1.00  0.00           C  
HETATM   11  O1  UNL     1       4.572   0.144  -0.321  1.00  0.00           O  
HETATM   12  O2  UNL     1       4.100  -1.445  -1.838  1.00  0.00           O  
HETATM   13  H1  UNL     1      -3.433   0.764  -1.999  1.00  0.00           H  
HETATM   14  H2  UNL     1      -2.399  -0.737  -2.186  1.00  0.00           H  
HETATM   15  H3  UNL     1      -1.682   0.840  -1.737  1.00  0.00           H  
HETATM   16  H4  UNL     1      -4.518   1.105   0.322  1.00  0.00           H  
HETATM   17  H5  UNL     1      -4.914  -0.581  -0.134  1.00  0.00           H  
HETATM   18  H6  UNL     1      -4.208  -0.248   1.465  1.00  0.00           H  
HETATM   19  H7  UNL     1      -2.011  -0.659   1.686  1.00  0.00           H  
HETATM   20  H8  UNL     1      -0.360  -0.500  -0.951  1.00  0.00           H  
HETATM   21  H9  UNL     1      -0.075  -1.661   0.392  1.00  0.00           H  
HETATM   22  H10 UNL     1       0.087   1.371   0.862  1.00  0.00           H  
HETATM   23  H11 UNL     1       0.374   0.030   1.988  1.00  0.00           H  
HETATM   24  H12 UNL     1       3.553   0.543   1.742  1.00  0.00           H  
HETATM   25  H13 UNL     1       2.304   1.821   1.974  1.00  0.00           H  
HETATM   26  H14 UNL     1       3.308   1.917   0.521  1.00  0.00           H  
HETATM   27  H15 UNL     1       1.579  -1.163  -0.916  1.00  0.00           H  
HETATM   28  H16 UNL     1       4.388  -2.385  -1.695  1.00  0.00           H  
CONECT    1    2   13   14   15
CONECT    2    3    4    4
CONECT    3   16   17   18
CONECT    4    5   19
CONECT    5    6   20   21
CONECT    6    7   22   23
CONECT    7    8    9    9
CONECT    8   24   25   26
CONECT    9   10   27
CONECT   10   11   11   12
CONECT   12   28
END

View in JSmol View Stereo Labels

Synonyms

Value	Source
Geranate	Generator
3,7-Dimethyl-2,6-octadienoic acid	HMDB
3,7-Dimethylocta-2,6-dienoate	HMDB, Generator
Decaprenoic acid	HMDB
Geranic acid (6ci)	HMDB
Geranoic acid	HMDB
trans-Geranate	Generator

Chemical Formula

C₁₀H₁₆O₂

Average Molecular Weight

168.2328

Monoisotopic Molecular Weight

168.115029756

IUPAC Name

3,7-dimethylocta-2,6-dienoic acid

Traditional Name

3,7-dimethylocta-2,6-dienoic acid

CAS Registry Number

459-80-3

SMILES

CC(C)=CCCC(C)=CC(O)=O

InChI Identifier

InChI=1S/C10H16O2/c1-8(2)5-4-6-9(3)7-10(11)12/h5,7H,4,6H2,1-3H3,(H,11,12)

InChI Key

ZHYZQXUYZJNEHD-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as acyclic monoterpenoids. These are monoterpenes that do not contain a cycle.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Monoterpenoids

Direct Parent

Acyclic monoterpenoids

Alternative Parents

Substituents

Acyclic monoterpenoid
Medium-chain fatty acid
Branched fatty acid
Methyl-branched fatty acid
Unsaturated fatty acid
Fatty acyl
Fatty acid
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic oxygen compound
Organooxygen compound
Carbonyl group
Hydrocarbon derivative
Organic oxide
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Route of exposure

Enteral

Ingestion (HMDB: HMDB0036103)

Source

Endogenous

Endogenous (HMDB: HMDB0036103)

Plant

Plant (HMDB: HMDB0036103)

Animal

Animal (HMDB: HMDB0036103)

Exogenous

Food

Food (HMDB: HMDB0036103)

Herb and spice

Spice

Ginger (FooDB: FOOD00206)

Tea

Process

Naturally occurring process

Biological process

Chemical reaction

Lipid Peroxidation (HMDB: HMDB0036103)

Biochemical pathway

Metabolic pathway

Fatty Acid Metabolism (HMDB: HMDB0036103)

Lipid metabolism pathway (HMDB: HMDB0036103)

Cellular process

Cell signaling (HMDB: HMDB0036103)

Biochemical process

Lipid transport (HMDB: HMDB0036103)

Role

Biological role

Energy source (HMDB: HMDB0036103)

Industrial application

Manufacturing industry

Material processing agent

Fluid processing agent

Surfactant

Surfactant (HMDB: HMDB0036103)

Physical Properties

State

Liquid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	21.00 °C. @ 760.00 mm Hg	The Good Scents Company Information System
Boiling Point	250.00 °C. @ 760.00 mm Hg	The Good Scents Company Information System
Water Solubility	108.2 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	3.066 (est)	The Good Scents Company Information System

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	1.22 g/L	ALOGPS
logP	2.72	ALOGPS
logP	2.82	ChemAxon
logS	-2.1	ALOGPS
pKa (Strongest Acidic)	5.26	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	37.3 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	51.05 m³·mol⁻¹	ChemAxon
Polarizability	19.53 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	141.751	31661259
DarkChem	[M-H]-	137.893	31661259
DeepCCS	[M+H]+	135.016	30932474
DeepCCS	[M-H]-	131.186	30932474
DeepCCS	[M-2H]-	168.228	30932474
DeepCCS	[M+Na]+	143.712	30932474
AllCCS	[M+H]+	139.4	32859911
AllCCS	[M+H-H2O]+	135.4	32859911
AllCCS	[M+NH4]+	143.1	32859911
AllCCS	[M+Na]+	144.2	32859911
AllCCS	[M-H]-	138.5	32859911
AllCCS	[M+Na-2H]-	140.1	32859911
AllCCS	[M+HCOO]-	141.9	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.	6.64 minutes	32390414
Predicted by Siyang on May 30, 2022	13.9008 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.64 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	2165.7 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	385.4 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	153.2 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	240.0 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	85.5 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	472.3 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	553.4 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	75.7 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1104.3 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	460.5 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	1123.4 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	338.0 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	362.3 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	347.8 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	410.6 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	18.5 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Geranic acid	CC(C)=CCCC(C)=CC(O)=O	2336.1	Standard polar	33892256
Geranic acid	CC(C)=CCCC(C)=CC(O)=O	1311.0	Standard non polar	33892256
Geranic acid	CC(C)=CCCC(C)=CC(O)=O	1367.7	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Geranic acid,1TMS,isomer #1	CC(C)=CCCC(C)=CC(=O)O[Si](C)(C)C	1447.1	Semi standard non polar	33892256
Geranic acid,1TBDMS,isomer #1	CC(C)=CCCC(C)=CC(=O)O[Si](C)(C)C(C)(C)C	1658.5	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 - Geranic acid GC-MS (Non-derivatized) - 70eV, Positive	splash10-066u-9300000000-0e5fa74a29642ffbea56	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Geranic acid GC-MS (1 TMS) - 70eV, Positive	splash10-0600-9510000000-c63599768f78d24aff89	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Geranic 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 - Geranic acid 10V, Positive-QTOF	splash10-0udi-0900000000-63a39683f1ee7ae411e1	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Geranic acid 20V, Positive-QTOF	splash10-0a4i-4900000000-69961fd8b0ac30801f92	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Geranic acid 40V, Positive-QTOF	splash10-066r-9000000000-5e0e3fc6d4f6195196b4	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Geranic acid 10V, Negative-QTOF	splash10-01b9-0900000000-2ca07626a0a6f2fc98fd	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Geranic acid 20V, Negative-QTOF	splash10-00xs-0900000000-f4de03fb18a11ded1779	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Geranic acid 40V, Negative-QTOF	splash10-0ab9-5900000000-140a8e79b9546d577420	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Geranic acid 10V, Negative-QTOF	splash10-014i-0900000000-d34b67d515962ee44c5f	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Geranic acid 20V, Negative-QTOF	splash10-00di-0900000000-e27ed5f74c7dd38be01b	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Geranic acid 40V, Negative-QTOF	splash10-0560-9400000000-4dadcf2bbe6fc51045cd	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Geranic acid 10V, Positive-QTOF	splash10-0159-9600000000-9f52332988cf28bfa12f	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Geranic acid 20V, Positive-QTOF	splash10-00lr-9000000000-29159b17a0fa9f011058	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Geranic acid 40V, Positive-QTOF	splash10-067l-9000000000-5dbb614d4e9125fa59e6	2021-09-24	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Extracellular
Membrane

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

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Geranic acid

METLIN ID

Not Available

PubChem Compound

5275520

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1001951

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
Watson AD: Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Lipidomics: a global approach to lipid analysis in biological systems. J Lipid Res. 2006 Oct;47(10):2101-11. Epub 2006 Aug 10. [PubMed:16902246 ]
Sethi JK, Vidal-Puig AJ: Thematic review series: adipocyte biology. Adipose tissue function and plasticity orchestrate nutritional adaptation. J Lipid Res. 2007 Jun;48(6):1253-62. Epub 2007 Mar 20. [PubMed:17374880 ]
Lingwood D, Simons K: Lipid rafts as a membrane-organizing principle. Science. 2010 Jan 1;327(5961):46-50. doi: 10.1126/science.1174621. [PubMed:20044567 ]
(). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .
Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.

Showing metabocard for Geranic acid (HMDB0036103)

MOL for HMDB0036103 (Geranic acid)

3D MOL for HMDB0036103 (Geranic acid)

3D SDF for HMDB0036103 (Geranic acid)

3D-SDF for HMDB0036103 (Geranic acid)

PDB for HMDB0036103 (Geranic acid)

3D PDB for HMDB0036103 (Geranic acid)

SMILES for HMDB0036103 (Geranic acid)

INCHI for HMDB0036103 (Geranic acid)

Structure for HMDB0036103 (Geranic acid)

3D Structure for HMDB0036103 (Geranic acid)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra