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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 20:53:49 UTC

Update Date

2021-09-26 23:16:16 UTC

HMDB ID

HMDB0259001

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Thiobarbital

Description

Thiobarbital belongs to the class of organic compounds known as thiobarbituric acid derivatives. These are organic compounds containing a 2-thioxodihydropyrimidine-4,6(1H,5H)-dione skeleton. Based on a literature review a significant number of articles have been published on Thiobarbital. This compound has been identified in human blood as reported by (PMID: 31557052 ). Thiobarbital is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Thiobarbital is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.

Structure

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

HEADER    PROTEIN                                 11-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-21         0                                  
HETATM    1  C   UNK     0      -1.173   3.222   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.344   3.490   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       4.001   2.310   0.000  0.00  0.00           O+0
HETATM    6  N   UNK     0       2.667  -0.000   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    8  S   UNK     0       1.334  -2.310   0.000  0.00  0.00           S+0
HETATM    9  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       2.324   3.490   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.797   4.937   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   10   12                                             
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9    3   11                                                  
CONECT   11   10                                                            
CONECT   12    3   13                                                       
CONECT   13   12                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   26    0
END

View in JSmol View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₈H₁₂N₂O₂S

Average Molecular Weight

200.26

Monoisotopic Molecular Weight

200.061948808

IUPAC Name

5,5-diethyl-2-sulfanylidene-1,3-diazinane-4,6-dione

Traditional Name

thiobarbital

CAS Registry Number

Not Available

SMILES

CCC1(CC)C(=O)NC(=S)NC1=O

InChI Identifier

InChI=1S/C8H12N2O2S/c1-3-8(4-2)5(11)9-7(13)10-6(8)12/h3-4H2,1-2H3,(H2,9,10,11,12,13)

InChI Key

QGVNJRROSLYGKF-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as thiobarbituric acid derivatives. These are organic compounds containing a 2-thioxodihydropyrimidine-4,6(1H,5H)-dione skeleton.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Diazines

Sub Class

Pyrimidines and pyrimidine derivatives

Direct Parent

Thiobarbituric acid derivatives

Alternative Parents

Substituents

Thiobarbiturate
1,3-diazinane
Thiourea
Azacycle
Carboxylic acid derivative
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organosulfur compound
Organooxygen compound
Organonitrogen compound
Carbonyl group
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Source

Exogenous

Exogenous (PMID: 31557052)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

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
logP	1.71	ALOGPS
logP	1.61	ChemAxon
logS	-2.4	ALOGPS
pKa (Strongest Acidic)	7.2	ChemAxon
pKa (Strongest Basic)	-8.4	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	58.2 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	52.24 m³·mol⁻¹	ChemAxon
Polarizability	19.89 Å³	ChemAxon
Number of Rings	1	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
DeepCCS	[M+H]+	139.904	30932474
DeepCCS	[M-H]-	136.073	30932474
DeepCCS	[M-2H]-	173.658	30932474
DeepCCS	[M+Na]+	149.197	30932474
AllCCS	[M+H]+	143.1	32859911
AllCCS	[M+H-H2O]+	139.0	32859911
AllCCS	[M+NH4]+	146.9	32859911
AllCCS	[M+Na]+	148.0	32859911
AllCCS	[M-H]-	142.8	32859911
AllCCS	[M+Na-2H]-	143.9	32859911
AllCCS	[M+HCOO]-	145.2	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.	4.4 minutes	32390414
Predicted by Siyang on May 30, 2022	13.8485 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.7 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	2254.1 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	436.7 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	152.9 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	283.6 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	191.9 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	439.2 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	796.9 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	137.7 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1051.6 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	421.3 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	1437.5 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	327.3 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	388.2 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	500.9 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	334.9 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	91.8 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Thiobarbital	CCC1(CC)C(=O)NC(=S)NC1=O	3233.7	Standard polar	33892256
Thiobarbital	CCC1(CC)C(=O)NC(=S)NC1=O	1669.3	Standard non polar	33892256
Thiobarbital	CCC1(CC)C(=O)NC(=S)NC1=O	1847.9	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Thiobarbital,1TMS,isomer #1	CCC1(CC)C(=O)NC(=S)N([Si](C)(C)C)C1=O	1675.4	Semi standard non polar	33892256
Thiobarbital,1TMS,isomer #1	CCC1(CC)C(=O)NC(=S)N([Si](C)(C)C)C1=O	1831.1	Standard non polar	33892256
Thiobarbital,1TMS,isomer #1	CCC1(CC)C(=O)NC(=S)N([Si](C)(C)C)C1=O	2817.3	Standard polar	33892256
Thiobarbital,2TMS,isomer #1	CCC1(CC)C(=O)N([Si](C)(C)C)C(=S)N([Si](C)(C)C)C1=O	1671.7	Semi standard non polar	33892256
Thiobarbital,2TMS,isomer #1	CCC1(CC)C(=O)N([Si](C)(C)C)C(=S)N([Si](C)(C)C)C1=O	1858.1	Standard non polar	33892256
Thiobarbital,2TMS,isomer #1	CCC1(CC)C(=O)N([Si](C)(C)C)C(=S)N([Si](C)(C)C)C1=O	2349.3	Standard polar	33892256
Thiobarbital,1TBDMS,isomer #1	CCC1(CC)C(=O)NC(=S)N([Si](C)(C)C(C)(C)C)C1=O	1883.0	Semi standard non polar	33892256
Thiobarbital,1TBDMS,isomer #1	CCC1(CC)C(=O)NC(=S)N([Si](C)(C)C(C)(C)C)C1=O	2071.3	Standard non polar	33892256
Thiobarbital,1TBDMS,isomer #1	CCC1(CC)C(=O)NC(=S)N([Si](C)(C)C(C)(C)C)C1=O	2886.0	Standard polar	33892256
Thiobarbital,2TBDMS,isomer #1	CCC1(CC)C(=O)N([Si](C)(C)C(C)(C)C)C(=S)N([Si](C)(C)C(C)(C)C)C1=O	2104.2	Semi standard non polar	33892256
Thiobarbital,2TBDMS,isomer #1	CCC1(CC)C(=O)N([Si](C)(C)C(C)(C)C)C(=S)N([Si](C)(C)C(C)(C)C)C1=O	2310.8	Standard non polar	33892256
Thiobarbital,2TBDMS,isomer #1	CCC1(CC)C(=O)N([Si](C)(C)C(C)(C)C)C(=S)N([Si](C)(C)C(C)(C)C)C1=O	2461.6	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Thiobarbital GC-MS (Non-derivatized) - 70eV, Positive	splash10-004i-9610000000-7c9c4976dd8a1756860e	2021-09-23	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Thiobarbital GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

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	Not Specified	Not Specified	Normal	31557052	details

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

Not Available

KNApSAcK ID

Not Available

Chemspider ID

580885

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Thiobarbital

METLIN ID

Not Available

PubChem Compound

6474

PDB ID

Not Available

ChEBI ID

Not Available

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

Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]

Showing metabocard for Thiobarbital (HMDB0259001)

MOL for HMDB0259001 (Thiobarbital)

3D MOL for HMDB0259001 (Thiobarbital)

3D SDF for HMDB0259001 (Thiobarbital)

3D-SDF for HMDB0259001 (Thiobarbital)

PDB for HMDB0259001 (Thiobarbital)

3D PDB for HMDB0259001 (Thiobarbital)

SMILES for HMDB0259001 (Thiobarbital)

INCHI for HMDB0259001 (Thiobarbital)

Structure for HMDB0259001 (Thiobarbital)

3D Structure for HMDB0259001 (Thiobarbital)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra