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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2012-09-11 19:04:53 UTC

Update Date

2023-02-21 17:24:08 UTC

HMDB ID

HMDB0034277

Secondary Accession Numbers

HMDB34277

Metabolite Identification

Common Name

Ligustilide

Description

Ligustilide belongs to the class of organic compounds known as isobenzofurans. These are organic aromatic compounds containing an isobenzofuran moiety. Ligustilide is found, on average, in the highest concentration within wild celeries (Apium graveolens). Ligustilide has also been detected, but not quantified in, a few different foods, such as celery stalks (Apium graveolens var. dulce), herbs and spices, and lovages (Levisticum officinale). This could make ligustilide a potential biomarker for the consumption of these foods. Based on a literature review a significant number of articles have been published on Ligustilide.

Structure

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

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0       3.235  -3.621   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.204  -2.477   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.680  -1.012   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.258   2.073   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.258   3.613   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.924   1.303   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.924   4.383   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.650   0.132   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.590   2.073   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.590   3.613   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.126   1.597   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.126   4.089   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       1.650   5.553   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       1.220   2.843   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    8                                                       
CONECT    4    5    6                                                       
CONECT    5    4    7                                                       
CONECT    6    4    9                                                       
CONECT    7    5   10                                                       
CONECT    8    3   11                                                       
CONECT    9    6   10   11                                                  
CONECT   10    7    9   12                                                  
CONECT   11    8    9   14                                                  
CONECT   12   10   13   14                                                  
CONECT   13   12                                                            
CONECT   14   11   12                                                       
MASTER        0    0    0    0    0    0    0    0   14    0   30    0
END

COMPND    HMDB0034277
HETATM    1  C1  UNL     1       3.684   1.354  -0.501  1.00  0.00           C  
HETATM    2  C2  UNL     1       2.995   0.045  -0.309  1.00  0.00           C  
HETATM    3  C3  UNL     1       1.884   0.171   0.787  1.00  0.00           C  
HETATM    4  C4  UNL     1       1.305  -1.153   0.870  1.00  0.00           C  
HETATM    5  C5  UNL     1       0.043  -1.459   0.668  1.00  0.00           C  
HETATM    6  O1  UNL     1      -0.464  -2.780   0.764  1.00  0.00           O  
HETATM    7  C6  UNL     1      -1.799  -2.702   0.493  1.00  0.00           C  
HETATM    8  O2  UNL     1      -2.585  -3.709   0.488  1.00  0.00           O  
HETATM    9  C7  UNL     1      -2.107  -1.303   0.227  1.00  0.00           C  
HETATM   10  C8  UNL     1      -1.031  -0.535   0.323  1.00  0.00           C  
HETATM   11  C9  UNL     1      -1.063   0.925   0.103  1.00  0.00           C  
HETATM   12  C10 UNL     1      -2.412   1.472  -0.234  1.00  0.00           C  
HETATM   13  C11 UNL     1      -3.522   0.531  -0.311  1.00  0.00           C  
HETATM   14  C12 UNL     1      -3.411  -0.748  -0.105  1.00  0.00           C  
HETATM   15  H1  UNL     1       4.590   1.356   0.162  1.00  0.00           H  
HETATM   16  H2  UNL     1       2.996   2.189  -0.235  1.00  0.00           H  
HETATM   17  H3  UNL     1       4.028   1.533  -1.530  1.00  0.00           H  
HETATM   18  H4  UNL     1       2.491  -0.234  -1.257  1.00  0.00           H  
HETATM   19  H5  UNL     1       3.669  -0.794  -0.052  1.00  0.00           H  
HETATM   20  H6  UNL     1       2.448   0.330   1.766  1.00  0.00           H  
HETATM   21  H7  UNL     1       1.344   1.023   0.483  1.00  0.00           H  
HETATM   22  H8  UNL     1       1.984  -2.006   1.129  1.00  0.00           H  
HETATM   23  H9  UNL     1      -0.744   1.487   1.018  1.00  0.00           H  
HETATM   24  H10 UNL     1      -0.434   1.196  -0.804  1.00  0.00           H  
HETATM   25  H11 UNL     1      -2.670   2.365   0.415  1.00  0.00           H  
HETATM   26  H12 UNL     1      -2.390   1.971  -1.269  1.00  0.00           H  
HETATM   27  H13 UNL     1      -4.529   0.893  -0.558  1.00  0.00           H  
HETATM   28  H14 UNL     1      -4.299  -1.418  -0.179  1.00  0.00           H  
CONECT    1    2   15   16   17
CONECT    2    3   18   19
CONECT    3    4   20   21
CONECT    4    5    5   22
CONECT    5    6   10
CONECT    6    7
CONECT    7    8    8    9
CONECT    9   10   10   14
CONECT   10   11
CONECT   11   12   23   24
CONECT   12   13   25   26
CONECT   13   14   14   27
CONECT   14   28
END

View in JSmol View Stereo Labels

Synonyms

Value	Source
(e)-Ligustilide	HMDB
3-Butylidene-4,5-dihydro-1(3H)-isobenzofuranone, 9ci	HMDB
3-Butylidene-4,5-dihydrophthalide, 8ci	HMDB
Z-Ligustilide	MeSH
Ligustilide, (e)-isomer	MeSH
Ligustilide, (Z)-isomer	MeSH
Ligustilide	MeSH

Chemical Formula

C₁₂H₁₄O₂

Average Molecular Weight

190.2384

Monoisotopic Molecular Weight

190.099379692

IUPAC Name

(3E)-3-butylidene-1,3,4,5-tetrahydro-2-benzofuran-1-one

Traditional Name

Z-ligustilide

CAS Registry Number

4431-01-0

SMILES

CCC\C=C1\OC(=O)C2=C1CCC=C2

InChI Identifier

InChI=1S/C12H14O2/c1-2-3-8-11-9-6-4-5-7-10(9)12(13)14-11/h5,7-8H,2-4,6H2,1H3/b11-8+

InChI Key

IQVQXVFMNOFTMU-DHZHZOJOSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as isobenzofurans. These are organic aromatic compounds containing an isobenzofuran moiety.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Isobenzofurans

Sub Class

Not Available

Direct Parent

Isobenzofurans

Alternative Parents

Substituents

Isobenzofuran
2-furanone
Dihydrofuran
Enol ester
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Carboxylic acid ester
Lactone
Carboxylic acid derivative
Oxacycle
Monocarboxylic acid or derivatives
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Organooxygen compound
Carbonyl group
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Membrane (HMDB: HMDB0034277)
Cell membrane (HMDB: HMDB0034277)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0034277)

Source

Exogenous

Exogenous (HMDB: HMDB0034277)

Food

Food (HMDB: HMDB0034277)

Herb and spice

Spice

Wild celery (FooDB: FOOD00015)

Herb

Lovage (FooDB: FOOD00100)

Herbs and Spices (FooDB: FOOD00866)

Vegetable

Stalk vegetable

Celery stalks (FooDB: FOOD00215)

Endogenous

Plant

Plant (HMDB: HMDB0034277)

Process

Not Available

Role

Biological role

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	377.00 to 378.00 °C. @ 760.00 mm Hg (est)	The Good Scents Company Information System
Water Solubility	125.7 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	1.710 (est)	The Good Scents Company Information System

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.5 g/L	ALOGPS
logP	3.48	ALOGPS
logP	2.73	ChemAxon
logS	-2.6	ALOGPS
pKa (Strongest Basic)	-7.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	1	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	26.3 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	58.04 m³·mol⁻¹	ChemAxon
Polarizability	21.14 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	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	146.481	31661259
DarkChem	[M-H]-	142.415	31661259
DeepCCS	[M+H]+	146.732	30932474
DeepCCS	[M-H]-	144.374	30932474
DeepCCS	[M-2H]-	179.084	30932474
DeepCCS	[M+Na]+	154.557	30932474
AllCCS	[M+H]+	143.6	32859911
AllCCS	[M+H-H2O]+	139.3	32859911
AllCCS	[M+NH4]+	147.5	32859911
AllCCS	[M+Na]+	148.7	32859911
AllCCS	[M-H]-	147.8	32859911
AllCCS	[M+Na-2H]-	148.2	32859911
AllCCS	[M+HCOO]-	148.7	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.	8.22 minutes	32390414
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.	7.5 minutes	32390414
Predicted by Siyang on May 30, 2022	18.9966 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	0.84 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	2688.8 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	606.7 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	247.1 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	440.3 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	341.9 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	798.9 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	736.1 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	139.6 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1647.0 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	568.1 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	1528.0 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	578.0 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	511.2 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	666.0 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	621.6 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	29.3 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Ligustilide	CCC\C=C1\OC(=O)C2=C1CCC=C2	2643.4	Standard polar	33892256
Ligustilide	CCC\C=C1\OC(=O)C2=C1CCC=C2	1752.9	Standard non polar	33892256
Ligustilide	CCC\C=C1\OC(=O)C2=C1CCC=C2	1729.4	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 - Ligustilide GC-MS (Non-derivatized) - 70eV, Positive	splash10-004l-6900000000-19a1ca647a7e0491d8e1	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Ligustilide GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Ligustilide 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 - Ligustilide 10V, Positive-QTOF	splash10-0006-3900000000-df63f7ba708218730e1c	2016-08-02	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ligustilide 20V, Positive-QTOF	splash10-0006-6900000000-bb0e90d13b2a41a2f252	2016-08-02	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ligustilide 40V, Positive-QTOF	splash10-0zi3-9100000000-a8552493184912c22439	2016-08-02	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ligustilide 10V, Negative-QTOF	splash10-000i-0900000000-da55f68b7672778c6684	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ligustilide 20V, Negative-QTOF	splash10-000j-1900000000-b2cafbc59a05197f25e3	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ligustilide 40V, Negative-QTOF	splash10-004l-8900000000-fc5da55ccfb2f546ca15	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ligustilide 10V, Positive-QTOF	splash10-0006-0900000000-02c830ea56178823e129	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ligustilide 20V, Positive-QTOF	splash10-000g-1900000000-ca00aa40e89649e134d3	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ligustilide 40V, Positive-QTOF	splash10-00or-9100000000-883a9cc29d1cd4ed674d	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ligustilide 10V, Negative-QTOF	splash10-000i-0900000000-f778b0a41733b7c667b1	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ligustilide 20V, Negative-QTOF	splash10-000i-0900000000-ce781099c44f51da042b	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ligustilide 40V, Negative-QTOF	splash10-05s1-3900000000-1cb74a6387e3878f4f59	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+Na]+)	2023-02-04	FELIX lab	View Spectrum

Biological Properties

Cellular Locations

Membrane

Biospecimen Locations

Blood
Urine

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Cancer patients undergoing total body irradiation	31424920	details
Urine	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Cancer patients undergoing total body irradiation	31424920	details

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

FDB012613

KNApSAcK ID

C00051275

Chemspider ID

4731467

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5877292

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1588231

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Lu Q, Qiu TQ, Yang H: Ligustilide inhibits vascular smooth muscle cells proliferation. Eur J Pharmacol. 2006 Aug 7;542(1-3):136-40. Epub 2006 May 11. [PubMed:16806164 ]
(). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .

Showing metabocard for Ligustilide (HMDB0034277)

MOL for HMDB0034277 (Ligustilide)

3D MOL for HMDB0034277 (Ligustilide)

3D SDF for HMDB0034277 (Ligustilide)

3D-SDF for HMDB0034277 (Ligustilide)

PDB for HMDB0034277 (Ligustilide)

3D PDB for HMDB0034277 (Ligustilide)

SMILES for HMDB0034277 (Ligustilide)

INCHI for HMDB0034277 (Ligustilide)

Structure for HMDB0034277 (Ligustilide)

3D Structure for HMDB0034277 (Ligustilide)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra

IR Spectra