Jump To Section:

Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References XML

Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 17:37:03 UTC

Update Date

2023-02-21 17:19:37 UTC

HMDB ID

HMDB0030481

Secondary Accession Numbers

HMDB30481

Metabolite Identification

Common Name

Agrocybin

Description

Agrocybin belongs to the class of organic compounds known as primary carboxylic acid amides. Primary carboxylic acid amides are compounds comprising primary carboxylic acid amide functional group, with the general structure RC(=O)NH2. Thus, agrocybin is considered to be a fatty amide. Based on a literature review very few articles have been published on Agrocybin.

Structure

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

View in JSmol View Stereo Labels

Synonyms

Value	Source
8-Hydroxy-2,4,6-octatriynamide	HMDB

Chemical Formula

C₈H₅NO₂

Average Molecular Weight

147.1308

Monoisotopic Molecular Weight

147.032028409

IUPAC Name

8-hydroxyocta-2,4,6-triynimidic acid

Traditional Name

8-hydroxyocta-2,4,6-triynimidic acid

CAS Registry Number

544-44-5

SMILES

OCC#CC#CC#CC(O)=N

InChI Identifier

InChI=1S/C8H5NO2/c9-8(11)6-4-2-1-3-5-7-10/h10H,7H2,(H2,9,11)

InChI Key

OXONWCQUZYDTNF-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as primary carboxylic acid amides. Primary carboxylic acid amides are compounds comprising primary carboxylic acid amide functional group, with the general structure RC(=O)NH2.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Carboxylic acid derivatives

Direct Parent

Primary carboxylic acid amides

Alternative Parents

Substituents

Primary carboxylic acid amide
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Organonitrogen compound
Carbonyl group
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Extracellular (HMDB: HMDB0030481)
Cytoplasm (HMDB: HMDB0030481)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0030481)

Source

Endogenous

Endogenous (HMDB: HMDB0030481)

Plant

Plant (HMDB: HMDB0030481)

Exogenous

Food

Food (HMDB: HMDB0030481)

Not Available

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	130 - 140 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	348100 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.056 g/L	ALOGPS
logP	0.47	ALOGPS
logP	0.7	ChemAxon
logS	-3.4	ALOGPS
pKa (Strongest Acidic)	6	ChemAxon
pKa (Strongest Basic)	3.89	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	64.31 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	52.95 m³·mol⁻¹	ChemAxon
Polarizability	15.47 Å³	ChemAxon
Number of Rings	0	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]+	138.66	31661259
DarkChem	[M-H]-	135.116	31661259
DeepCCS	[M+H]+	122.274	30932474
DeepCCS	[M-H]-	120.327	30932474
DeepCCS	[M-2H]-	156.555	30932474
DeepCCS	[M+Na]+	131.153	30932474
AllCCS	[M+H]+	129.5	32859911
AllCCS	[M+H-H2O]+	125.4	32859911
AllCCS	[M+NH4]+	133.4	32859911
AllCCS	[M+Na]+	134.5	32859911
AllCCS	[M-H]-	127.7	32859911
AllCCS	[M+Na-2H]-	129.2	32859911
AllCCS	[M+HCOO]-	131.0	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Agrocybin	OCC#CC#CC#CC(O)=N	2623.2	Standard polar	33892256
Agrocybin	OCC#CC#CC#CC(O)=N	1555.1	Standard non polar	33892256
Agrocybin	OCC#CC#CC#CC(O)=N	1741.0	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Agrocybin,1TMS,isomer #1	C[Si](C)(C)OCC#CC#CC#CC(=N)O	1818.7	Semi standard non polar	33892256
Agrocybin,1TMS,isomer #2	C[Si](C)(C)OC(=N)C#CC#CC#CCO	1801.7	Semi standard non polar	33892256
Agrocybin,1TMS,isomer #3	C[Si](C)(C)N=C(O)C#CC#CC#CCO	1826.6	Semi standard non polar	33892256
Agrocybin,2TMS,isomer #1	C[Si](C)(C)OCC#CC#CC#CC(=N)O[Si](C)(C)C	1985.5	Semi standard non polar	33892256
Agrocybin,2TMS,isomer #2	C[Si](C)(C)N=C(O)C#CC#CC#CCO[Si](C)(C)C	1944.2	Semi standard non polar	33892256
Agrocybin,2TMS,isomer #3	C[Si](C)(C)N=C(C#CC#CC#CCO)O[Si](C)(C)C	1888.5	Semi standard non polar	33892256
Agrocybin,3TMS,isomer #1	C[Si](C)(C)N=C(C#CC#CC#CCO[Si](C)(C)C)O[Si](C)(C)C	1995.1	Semi standard non polar	33892256
Agrocybin,3TMS,isomer #1	C[Si](C)(C)N=C(C#CC#CC#CCO[Si](C)(C)C)O[Si](C)(C)C	1824.2	Standard non polar	33892256
Agrocybin,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC#CC#CC#CC(=N)O	2052.6	Semi standard non polar	33892256
Agrocybin,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC(=N)C#CC#CC#CCO	2044.5	Semi standard non polar	33892256
Agrocybin,1TBDMS,isomer #3	CC(C)(C)[Si](C)(C)N=C(O)C#CC#CC#CCO	2023.8	Semi standard non polar	33892256
Agrocybin,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC#CC#CC#CC(=N)O[Si](C)(C)C(C)(C)C	2423.4	Semi standard non polar	33892256
Agrocybin,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N=C(O)C#CC#CC#CCO[Si](C)(C)C(C)(C)C	2381.1	Semi standard non polar	33892256
Agrocybin,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)N=C(C#CC#CC#CCO)O[Si](C)(C)C(C)(C)C	2380.4	Semi standard non polar	33892256
Agrocybin,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N=C(C#CC#CC#CCO[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	2645.3	Semi standard non polar	33892256
Agrocybin,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N=C(C#CC#CC#CCO[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	2475.7	Standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Agrocybin GC-MS (Non-derivatized) - 70eV, Positive	splash10-0ged-3900000000-91fd946ab5d60fe2296a	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Agrocybin GC-MS (2 TMS) - 70eV, Positive	splash10-00di-9370000000-551199b8897584f19a1f	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Agrocybin 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 - Agrocybin 10V, Positive-QTOF	splash10-000t-0900000000-2ee2b84cfa973832e1ca	2015-04-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Agrocybin 20V, Positive-QTOF	splash10-001i-0900000000-eb4002931ddc27043c50	2015-04-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Agrocybin 40V, Positive-QTOF	splash10-0udi-7900000000-c80403cc6f72fd3e44da	2015-04-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Agrocybin 10V, Negative-QTOF	splash10-0002-0900000000-76246977139b6db8b140	2015-04-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Agrocybin 20V, Negative-QTOF	splash10-00kb-4900000000-0e290a18c738ecbb48b8	2015-04-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Agrocybin 40V, Negative-QTOF	splash10-0006-9100000000-b38b9045974c939cbbb7	2015-04-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Agrocybin 10V, Positive-QTOF	splash10-001i-2900000000-b1165e205043569d2368	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Agrocybin 20V, Positive-QTOF	splash10-000i-9400000000-883a06bcb9761fb75b82	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Agrocybin 40V, Positive-QTOF	splash10-0079-9000000000-ef91196f883beec97c9d	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Agrocybin 10V, Negative-QTOF	splash10-0002-0900000000-df53a7fe954012d2c807	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Agrocybin 20V, Negative-QTOF	splash10-0fk9-9500000000-ee132b8d5c656a70c9d1	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Agrocybin 40V, Negative-QTOF	splash10-0006-9000000000-1e1957d424a108e3ca6e	2021-09-22	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]-)	2023-02-03	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)	2023-02-03	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

FDB002350

KNApSAcK ID

C00021684

Chemspider ID

10538

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11004

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1820321

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 Agrocybin (HMDB0030481)

MOL for HMDB0030481 (Agrocybin)

3D MOL for HMDB0030481 (Agrocybin)

3D SDF for HMDB0030481 (Agrocybin)

3D-SDF for HMDB0030481 (Agrocybin)

PDB for HMDB0030481 (Agrocybin)

3D PDB for HMDB0030481 (Agrocybin)

SMILES for HMDB0030481 (Agrocybin)

INCHI for HMDB0030481 (Agrocybin)

Structure for HMDB0030481 (Agrocybin)

3D Structure for HMDB0030481 (Agrocybin)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

IR Spectra