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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-06 15:16:49 UTC
Update Date2021-10-13 05:43:35 UTC
HMDB IDHMDB0014457
Secondary Accession Numbers
  • HMDB14457
Metabolite Identification
Common NamePentobarbital
DescriptionPentobarbital, also known as nembutal or pentobarbitone, belongs to the class of organic compounds known as pyrimidones. Pyrimidones are compounds that contain a pyrimidine ring, which bears a ketone. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions. Pentobarbital is a drug which is used for the short-term treatment of insomnia. Based on a literature review a significant number of articles have been published on Pentobarbital.
Structure
Data?1582753182
Synonyms
ValueSource
5-Ethyl-5-(1-methyl-butyl)-pyrimidine-2,4,6-trioneChEBI
5-Ethyl-5-(1-methylbutyl)-2,4,6(1H,3H,5H)-pyrimidinetrioneChEBI
5-Ethyl-5-(1-methylbutyl)barbituric acidChEBI
5-Ethyl-5-(sec-pentyl)barbituric acidChEBI
NembutalChEBI
PentobarbitoneChEBI
5-Ethyl-5-(1-methylbutyl)barbitateGenerator
5-Ethyl-5-(1-methylbutyl)barbitic acidGenerator
5-Ethyl-5-(sec-pentyl)barbitateGenerator
5-Ethyl-5-(sec-pentyl)barbitic acidGenerator
PentabarbitalHMDB
PentabarbitoneHMDB
PentobarbiturateHMDB
Pentobarbituric acidHMDB
Sodium pentobarbitalHMDB
EtaminalMeSH, HMDB
EthaminalMeSH, HMDB
Pentobarbital sodiumMeSH, HMDB
SagatalMeSH, HMDB
DiabutalMeSH, HMDB
Pentobarbital, monosodium saltMeSH, HMDB
MebubarbitalMeSH, HMDB
MebumalMeSH, HMDB
Monosodium salt pentobarbitalMeSH, HMDB
Chemical FormulaC11H18N2O3
Average Molecular Weight226.2722
Monoisotopic Molecular Weight226.131742452
IUPAC Name5-ethyl-5-(pentan-2-yl)-1,3-diazinane-2,4,6-trione
Traditional Namepentobarbital
CAS Registry Number76-74-4
SMILES
CCCC(C)C1(CC)C(=O)NC(=O)NC1=O
InChI Identifier
InChI=1S/C11H18N2O3/c1-4-6-7(3)11(5-2)8(14)12-10(16)13-9(11)15/h7H,4-6H2,1-3H3,(H2,12,13,14,15,16)
InChI KeyWEXRUCMBJFQVBZ-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyrimidones. Pyrimidones are compounds that contain a pyrimidine ring, which bears a ketone. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassDiazines
Sub ClassPyrimidines and pyrimidine derivatives
Direct ParentPyrimidones
Alternative Parents
Substituents
  • Pyrimidone
  • Hydropyrimidine
  • 2,5-dihydropyrimidine
  • Carbonic acid derivative
  • Propargyl-type 1,3-dipolar organic compound
  • Organic 1,3-dipolar compound
  • Azacycle
  • Organic oxide
  • Organooxygen compound
  • Organonitrogen compound
  • Organopnictogen compound
  • Organic oxygen compound
  • Carbonyl group
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
Disposition

Biological location

Source

Route of exposure

Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point129.5 °CNot Available
Boiling Point226.50 °C. @ 760.00 mm Hg (est)The Good Scents Company Information System
Water Solubility0.86 g/LNot Available
LogP2.1Not Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.86 g/LALOGPS
logP10(2.16) g/LALOGPS
logP10(1.89) g/LChemAxon
logS10(-2.4) g/LALOGPS
pKa (Strongest Acidic)8.48ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area75.27 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity58 m³·mol⁻¹ChemAxon
Polarizability23.41 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+153.59731661259
DarkChem[M-H]-149.23131661259
DeepCCS[M+H]+153.6230932474
DeepCCS[M-H]-149.79330932474

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
PentobarbitalCCCC(C)C1(CC)C(=O)NC(=O)NC1=O2987.8Standard polar33892256
PentobarbitalCCCC(C)C1(CC)C(=O)NC(=O)NC1=O1697.5Standard non polar33892256
PentobarbitalCCCC(C)C1(CC)C(=O)NC(=O)NC1=O1726.6Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Pentobarbital,1TMS,isomer #1CCCC(C)C1(CC)C(=O)NC(=O)N([Si](C)(C)C)C1=O1699.4Semi standard non polar33892256
Pentobarbital,1TMS,isomer #1CCCC(C)C1(CC)C(=O)NC(=O)N([Si](C)(C)C)C1=O1879.2Standard non polar33892256
Pentobarbital,1TMS,isomer #1CCCC(C)C1(CC)C(=O)NC(=O)N([Si](C)(C)C)C1=O2756.0Standard polar33892256
Pentobarbital,2TMS,isomer #1CCCC(C)C1(CC)C(=O)N([Si](C)(C)C)C(=O)N([Si](C)(C)C)C1=O1686.4Semi standard non polar33892256
Pentobarbital,2TMS,isomer #1CCCC(C)C1(CC)C(=O)N([Si](C)(C)C)C(=O)N([Si](C)(C)C)C1=O1921.9Standard non polar33892256
Pentobarbital,2TMS,isomer #1CCCC(C)C1(CC)C(=O)N([Si](C)(C)C)C(=O)N([Si](C)(C)C)C1=O2286.6Standard polar33892256
Pentobarbital,1TBDMS,isomer #1CCCC(C)C1(CC)C(=O)NC(=O)N([Si](C)(C)C(C)(C)C)C1=O1908.7Semi standard non polar33892256
Pentobarbital,1TBDMS,isomer #1CCCC(C)C1(CC)C(=O)NC(=O)N([Si](C)(C)C(C)(C)C)C1=O2107.2Standard non polar33892256
Pentobarbital,1TBDMS,isomer #1CCCC(C)C1(CC)C(=O)NC(=O)N([Si](C)(C)C(C)(C)C)C1=O2785.1Standard polar33892256
Pentobarbital,2TBDMS,isomer #1CCCC(C)C1(CC)C(=O)N([Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C1=O2115.0Semi standard non polar33892256
Pentobarbital,2TBDMS,isomer #1CCCC(C)C1(CC)C(=O)N([Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C1=O2357.2Standard non polar33892256
Pentobarbital,2TBDMS,isomer #1CCCC(C)C1(CC)C(=O)N([Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C1=O2435.5Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental GC-MSGC-MS Spectrum - Pentobarbital CI-B (Non-derivatized)splash10-004i-0090000000-0f97406e79f836abc0742017-09-12HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Pentobarbital EI-B (Non-derivatized)splash10-0a4l-5900000000-08245bcc95f52792c8632017-09-12HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Pentobarbital CI-B (Non-derivatized)splash10-004i-0090000000-0f97406e79f836abc0742018-05-18HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Pentobarbital EI-B (Non-derivatized)splash10-0a4l-5900000000-08245bcc95f52792c8632018-05-18HMDB team, MONA, MassBankView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Pentobarbital GC-MS (Non-derivatized) - 70eV, Positivesplash10-01xy-9720000000-ebfd954ba228514ca3472017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Pentobarbital GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Pentobarbital GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Pentobarbital GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
MSMass Spectrum (Electron Ionization)splash10-0a4l-6900000000-a65d8c67e006ad4488142014-09-20Not AvailableView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pentobarbital 10V, Positive-QTOFsplash10-004i-1290000000-90bfbd79bea4fe2b007b2015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pentobarbital 20V, Positive-QTOFsplash10-0bti-1900000000-7e31dcdb272669c131012015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pentobarbital 40V, Positive-QTOFsplash10-01bc-9100000000-c9fe8276b8137dc73d202015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pentobarbital 10V, Negative-QTOFsplash10-004i-3980000000-84ea889a0fae4bed224b2015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pentobarbital 20V, Negative-QTOFsplash10-0006-9500000000-c226fe2dfb4ee13e4ae82015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pentobarbital 40V, Negative-QTOFsplash10-000x-9500000000-cd4190b9c110ee5e44282015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pentobarbital 10V, Positive-QTOFsplash10-0a4i-0930000000-ce337224a05a5827ddf42021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pentobarbital 20V, Positive-QTOFsplash10-0a4i-1910000000-61c3bd30210f2bd150342021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pentobarbital 40V, Positive-QTOFsplash10-0aos-6900000000-cd89b663334e7901acd12021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pentobarbital 10V, Negative-QTOFsplash10-004i-1390000000-b300ae41f3e7623fa8822021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pentobarbital 20V, Negative-QTOFsplash10-0006-9000000000-b2af88d76179b34025702021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pentobarbital 40V, Negative-QTOFsplash10-0006-9300000000-99ecf1568fa04b732c332021-09-23Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Membrane
Biospecimen Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableTaking drug identified by DrugBank entry DB00312 details
UrineExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableTaking drug identified by DrugBank entry DB00312 details
Abnormal Concentrations
Not Available
Predicted Concentrations
BiospecimenValueOriginal ageOriginal sexOriginal conditionComments
Blood0.000 uMAdult (>18 years old)BothNormalPredicted based on drug qualities
Blood0.000 umol/mmol creatinineAdult (>18 years old)BothNormalPredicted based on drug qualities
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB00312
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID4575
KEGG Compound IDC07422
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkPentobarbital
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID7983
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1621031
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Knodell RG, Spector MH, Brooks DA, Keller FX, Kyner WT: Alterations in pentobarbital pharmacokinetics in response to parenteral and enteral alimentation in the rat. Gastroenterology. 1980 Dec;79(6):1211-6. [PubMed:6777235 ]

Enzymes

General function:
Involved in monooxygenase activity
Specific function:
Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It performs a variety of oxidation reactions (e.g. caffeine 8-oxidation, omeprazole sulphoxidation, midazolam 1'-hydroxylation and midazolam 4-hydroxylation) of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. Acts as a 1,8-cineole 2-exo-monooxygenase. The enzyme also hydroxylates etoposide.
Gene Name:
CYP3A4
Uniprot ID:
P08684
Molecular weight:
57255.585
General function:
Involved in monooxygenase activity
Specific function:
Responsible for the metabolism of a number of therapeutic agents such as the anticonvulsant drug S-mephenytoin, omeprazole, proguanil, certain barbiturates, diazepam, propranolol, citalopram and imipramine.
Gene Name:
CYP2C19
Uniprot ID:
P33261
Molecular weight:
55944.565
References
  1. Preissner S, Kroll K, Dunkel M, Senger C, Goldsobel G, Kuzman D, Guenther S, Winnenburg R, Schroeder M, Preissner R: SuperCYP: a comprehensive database on Cytochrome P450 enzymes including a tool for analysis of CYP-drug interactions. Nucleic Acids Res. 2010 Jan;38(Database issue):D237-43. doi: 10.1093/nar/gkp970. Epub 2009 Nov 24. [PubMed:19934256 ]
General function:
Involved in ionotropic glutamate receptor activity
Specific function:
Ionotropic glutamate receptor. L-glutamate acts as an excitatory neurotransmitter at many synapses in the central nervous system. Binding of the excitatory neurotransmitter L- glutamate induces a conformation change, leading to the opening of the cation channel, and thereby converts the chemical signal to an electrical impulse. The receptor then desensitizes rapidly and enters a transient inactive state, characterized by the presence of bound agonist. May be involved in the transmission of light information from the retina to the hypothalamus. Modulates cell surface expression of NETO2
Gene Name:
GRIK2
Uniprot ID:
Q13002
Molecular weight:
102582.5
References
  1. Yamakura T, Bertaccini E, Trudell JR, Harris RA: Anesthetics and ion channels: molecular models and sites of action. Annu Rev Pharmacol Toxicol. 2001;41:23-51. [PubMed:11264449 ]
  2. Krasowski MD, Harrison NL: General anaesthetic actions on ligand-gated ion channels. Cell Mol Life Sci. 1999 Aug 15;55(10):1278-303. [PubMed:10487207 ]
General function:
Involved in ionotropic glutamate receptor activity
Specific function:
Ionotropic glutamate receptor. L-glutamate acts as an excitatory neurotransmitter at many synapses in the central nervous system. Binding of the excitatory neurotransmitter L- glutamate induces a conformation change, leading to the opening of the cation channel, and thereby converts the chemical signal to an electrical impulse. The receptor then desensitizes rapidly and enters a transient inactive state, characterized by the presence of bound agonist
Gene Name:
GRIA2
Uniprot ID:
P42262
Molecular weight:
98820.3
References
  1. Yamakura T, Bertaccini E, Trudell JR, Harris RA: Anesthetics and ion channels: molecular models and sites of action. Annu Rev Pharmacol Toxicol. 2001;41:23-51. [PubMed:11264449 ]
  2. Krasowski MD, Harrison NL: General anaesthetic actions on ligand-gated ion channels. Cell Mol Life Sci. 1999 Aug 15;55(10):1278-303. [PubMed:10487207 ]
General function:
Involved in ion transport
Specific function:
GABA, the major inhibitory neurotransmitter in the vertebrate brain, mediates neuronal inhibition by binding to the GABA/benzodiazepine receptor and opening an integral chloride channel
Gene Name:
GABRA1
Uniprot ID:
P14867
Molecular weight:
51801.4
References
  1. Steinbach JH, Akk G: Modulation of GABA(A) receptor channel gating by pentobarbital. J Physiol. 2001 Dec 15;537(Pt 3):715-33. [PubMed:11744750 ]
  2. Whiting PJ: The GABAA receptor gene family: new opportunities for drug development. Curr Opin Drug Discov Devel. 2003 Sep;6(5):648-57. [PubMed:14579514 ]
  3. Mehta AK, Ticku MK: An update on GABAA receptors. Brain Res Brain Res Rev. 1999 Apr;29(2-3):196-217. [PubMed:10209232 ]
  4. Krasowski MD, Harrison NL: General anaesthetic actions on ligand-gated ion channels. Cell Mol Life Sci. 1999 Aug 15;55(10):1278-303. [PubMed:10487207 ]
  5. Yamakura T, Bertaccini E, Trudell JR, Harris RA: Anesthetics and ion channels: molecular models and sites of action. Annu Rev Pharmacol Toxicol. 2001;41:23-51. [PubMed:11264449 ]
  6. Davies DL, McCauley LD, Bolger MB, Alkana RL: Pressure-sensitive and -insensitive coupling in gamma-aminobutyric acid(A) receptors. Psychopharmacology (Berl). 2001 Oct;157(4):401-10. [PubMed:11605100 ]
  7. Rahman M, Zhu D, Lindblad C, Johansson IM, Holmberg E, Isaksson M, Taube M, Backstrom T, Wang MD: GABA-site antagonism and pentobarbital actions do not depend on the alpha-subunit type in the recombinant rat GABA receptor. Acta Physiol (Oxf). 2006 Aug;187(4):479-88. [PubMed:16866778 ]
  8. Feigenspan A, Weiler R: Electrophysiological properties of mouse horizontal cell GABAA receptors. J Neurophysiol. 2004 Nov;92(5):2789-801. Epub 2004 Jul 7. [PubMed:15240758 ]
  9. Chen X, Ji ZL, Chen YZ: TTD: Therapeutic Target Database. Nucleic Acids Res. 2002 Jan 1;30(1):412-5. [PubMed:11752352 ]
  10. Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [PubMed:17139284 ]
  11. Imming P, Sinning C, Meyer A: Drugs, their targets and the nature and number of drug targets. Nat Rev Drug Discov. 2006 Oct;5(10):821-34. [PubMed:17016423 ]
General function:
Involved in ion transport
Specific function:
GABA, the major inhibitory neurotransmitter in the vertebrate brain, mediates neuronal inhibition by binding to the GABA/benzodiazepine receptor and opening an integral chloride channel
Gene Name:
GABRA2
Uniprot ID:
P47869
Molecular weight:
51325.9
References
  1. Yamakura T, Bertaccini E, Trudell JR, Harris RA: Anesthetics and ion channels: molecular models and sites of action. Annu Rev Pharmacol Toxicol. 2001;41:23-51. [PubMed:11264449 ]
  2. Mehta AK, Ticku MK: An update on GABAA receptors. Brain Res Brain Res Rev. 1999 Apr;29(2-3):196-217. [PubMed:10209232 ]
General function:
Involved in ion transport
Specific function:
GABA, the major inhibitory neurotransmitter in the vertebrate brain, mediates neuronal inhibition by binding to the GABA/benzodiazepine receptor and opening an integral chloride channel
Gene Name:
GABRA3
Uniprot ID:
P34903
Molecular weight:
55164.1
References
  1. Yamakura T, Bertaccini E, Trudell JR, Harris RA: Anesthetics and ion channels: molecular models and sites of action. Annu Rev Pharmacol Toxicol. 2001;41:23-51. [PubMed:11264449 ]
  2. Mehta AK, Ticku MK: An update on GABAA receptors. Brain Res Brain Res Rev. 1999 Apr;29(2-3):196-217. [PubMed:10209232 ]
General function:
Involved in ion transport
Specific function:
GABA, the major inhibitory neurotransmitter in the vertebrate brain, mediates neuronal inhibition by binding to the GABA/benzodiazepine receptor and opening an integral chloride channel
Gene Name:
GABRA4
Uniprot ID:
P48169
Molecular weight:
61622.6
References
  1. Mehta AK, Ticku MK: An update on GABAA receptors. Brain Res Brain Res Rev. 1999 Apr;29(2-3):196-217. [PubMed:10209232 ]
General function:
Involved in ion transport
Specific function:
GABA, the major inhibitory neurotransmitter in the vertebrate brain, mediates neuronal inhibition by binding to the GABA/benzodiazepine receptor and opening an integral chloride channel
Gene Name:
GABRA5
Uniprot ID:
P31644
Molecular weight:
52145.6
References
  1. Yamakura T, Bertaccini E, Trudell JR, Harris RA: Anesthetics and ion channels: molecular models and sites of action. Annu Rev Pharmacol Toxicol. 2001;41:23-51. [PubMed:11264449 ]
  2. Mehta AK, Ticku MK: An update on GABAA receptors. Brain Res Brain Res Rev. 1999 Apr;29(2-3):196-217. [PubMed:10209232 ]
General function:
Involved in ion transport
Specific function:
GABA, the major inhibitory neurotransmitter in the vertebrate brain, mediates neuronal inhibition by binding to the GABA/benzodiazepine receptor and opening an integral chloride channel
Gene Name:
GABRA6
Uniprot ID:
Q16445
Molecular weight:
51023.7
References
  1. Mehta AK, Ticku MK: An update on GABAA receptors. Brain Res Brain Res Rev. 1999 Apr;29(2-3):196-217. [PubMed:10209232 ]
  2. Yamakura T, Bertaccini E, Trudell JR, Harris RA: Anesthetics and ion channels: molecular models and sites of action. Annu Rev Pharmacol Toxicol. 2001;41:23-51. [PubMed:11264449 ]