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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 17:36:28 UTC

Update Date

2023-02-21 17:19:34 UTC

HMDB ID

HMDB0030383

Secondary Accession Numbers

HMDB30383

Metabolite Identification

Common Name

Zapotidine

Description

Zapotidine belongs to the class of organic compounds known as pyrimidinethiones. Pyrimidinethiones are compounds containing a pyrimidine ring that bears a thioketone. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions. Based on a literature review very few articles have been published on Zapotidine.

Structure

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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
6-Methylimidazo[1,5-c]tetrahydropyrimidine-5-thione	HMDB

Chemical Formula

C₇H₉N₃S

Average Molecular Weight

167.231

Monoisotopic Molecular Weight

167.051717993

IUPAC Name

6-methyl-5H,6H,7H,8H-imidazo[1,5-c]pyrimidine-5-thione

Traditional Name

6-methyl-7H,8H-imidazo[1,5-c]pyrimidine-5-thione

CAS Registry Number

525-84-8

SMILES

CN1CCC2=CN=CN2C1=S

InChI Identifier

InChI=1S/C7H9N3S/c1-9-3-2-6-4-8-5-10(6)7(9)11/h4-5H,2-3H2,1H3

InChI Key

OXVNSOXLMCVHBU-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrimidinethiones. Pyrimidinethiones are compounds containing a pyrimidine ring that bears a thioketone. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Diazines

Sub Class

Pyrimidines and pyrimidine derivatives

Direct Parent

Pyrimidinethiones

Alternative Parents

Substituents

Pyrimidinethione
N-substituted imidazole
Heteroaromatic compound
Imidazole
Azole
Thiourea
Azacycle
Organic nitrogen compound
Organopnictogen compound
Hydrocarbon derivative
Organosulfur compound
Organonitrogen 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: HMDB0030383)
Cytoplasm (HMDB: HMDB0030383)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0030383)

Source

Endogenous

Endogenous (HMDB: HMDB0030383)

Plant

Plant (HMDB: HMDB0030383)

Exogenous

Food

Food (HMDB: HMDB0030383)

Fruit

Pome

Pomes (FooDB: FOOD00856)

Exogenous (HMDB: HMDB0030383)

Process

Not Available

Role

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	96 - 98 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	4.0e-05 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	0.9 g/L	ALOGPS
logP	0.63	ALOGPS
logP	-0.091	ChemAxon
logS	-2.3	ALOGPS
pKa (Strongest Basic)	2.75	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	1	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	21.06 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	48.04 m³·mol⁻¹	ChemAxon
Polarizability	17.25 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]+	136.459	31661259
DarkChem	[M-H]-	130.901	31661259
DeepCCS	[M+H]+	132.327	30932474
DeepCCS	[M-H]-	130.286	30932474
DeepCCS	[M-2H]-	165.844	30932474
DeepCCS	[M+Na]+	140.062	30932474
AllCCS	[M+H]+	134.2	32859911
AllCCS	[M+H-H2O]+	129.7	32859911
AllCCS	[M+NH4]+	138.4	32859911
AllCCS	[M+Na]+	139.6	32859911
AllCCS	[M-H]-	133.8	32859911
AllCCS	[M+Na-2H]-	134.9	32859911
AllCCS	[M+HCOO]-	136.3	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.	3.5 minutes	32390414
Predicted by Siyang on May 30, 2022	8.5317 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.43 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	301.2 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	329.7 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	281.2 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	69.0 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	181.7 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	46.7 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	280.0 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	257.2 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	960.8 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	543.7 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	38.7 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	698.7 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	195.2 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	192.1 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	791.3 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	671.4 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	200.3 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Zapotidine	CN1CCC2=CN=CN2C1=S	2689.7	Standard polar	33892256
Zapotidine	CN1CCC2=CN=CN2C1=S	1611.9	Standard non polar	33892256
Zapotidine	CN1CCC2=CN=CN2C1=S	1979.1	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 - Zapotidine GC-MS (Non-derivatized) - 70eV, Positive	splash10-0006-9800000000-bde83e9b61d4c6f191cd	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Zapotidine 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 - Zapotidine 10V, Positive-QTOF	splash10-014i-0900000000-da7bfe002b4939b7dfd6	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Zapotidine 20V, Positive-QTOF	splash10-014i-2900000000-f3d878aa71ae7d4e1562	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Zapotidine 40V, Positive-QTOF	splash10-014i-9000000000-4e7cee26537894d1c96a	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Zapotidine 10V, Negative-QTOF	splash10-014i-0900000000-a7751a392f1e7768da84	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Zapotidine 20V, Negative-QTOF	splash10-01b9-2900000000-f2ec497606fffcb2f779	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Zapotidine 40V, Negative-QTOF	splash10-00xr-9000000000-fe1eed7c9c95124b6984	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Zapotidine 10V, Negative-QTOF	splash10-014i-0900000000-442a5b724daac476ef18	2021-09-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Zapotidine 20V, Negative-QTOF	splash10-014i-0900000000-5d3e3c773fa194c668c6	2021-09-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Zapotidine 40V, Negative-QTOF	splash10-014l-9500000000-52a89d7abefb23c5852f	2021-09-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Zapotidine 10V, Positive-QTOF	splash10-014i-0900000000-a5bdf3f7b0c631013b75	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Zapotidine 20V, Positive-QTOF	splash10-014i-0900000000-0fbb2062ed62805f156d	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Zapotidine 40V, Positive-QTOF	splash10-000x-9300000000-be10173372c3ff2c5528	2021-09-25	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-30	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+Na]+)	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

FDB002234

KNApSAcK ID

C00025547

Chemspider ID

30776830

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

12445018

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1880061

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 Zapotidine (HMDB0030383)

MOL for HMDB0030383 (Zapotidine)

3D MOL for HMDB0030383 (Zapotidine)

3D SDF for HMDB0030383 (Zapotidine)

3D-SDF for HMDB0030383 (Zapotidine)

PDB for HMDB0030383 (Zapotidine)

3D PDB for HMDB0030383 (Zapotidine)

SMILES for HMDB0030383 (Zapotidine)

INCHI for HMDB0030383 (Zapotidine)

Structure for HMDB0030383 (Zapotidine)

3D Structure for HMDB0030383 (Zapotidine)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra