Hmdb loader
You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Human Metabolome Database.
Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2013-05-17 01:23:18 UTC
Update Date2021-09-14 15:45:49 UTC
HMDB IDHMDB0060472
Secondary Accession Numbers
  • HMDB60472
Metabolite Identification
Common NameDidemethylcitalopram
DescriptionDidemethylcitalopram belongs to the class of organic compounds known as phenylbutylamines. Phenylbutylamines are compounds containing a phenylbutylamine moiety, which consists of a phenyl group substituted at the fourth carbon by an butan-1-amine. Didemethylcitalopram is a very strong basic compound (based on its pKa). Didemethylcitalopram exists in all living organisms, ranging from bacteria to humans. Within humans, didemethylcitalopram participates in a number of enzymatic reactions. In particular, didemethylcitalopram can be converted into citalopram aldehyde through the action of the enzymes amine oxidase [flavin-containing] a and amine oxidase [flavin-containing] b. In addition, didemethylcitalopram and formaldehyde can be biosynthesized from N-desmethylcitalopram; which is mediated by the enzyme cytochrome P450 2D6. In humans, didemethylcitalopram is involved in citalopram metabolism pathway.
Structure
Data?1563866064
Synonyms
ValueSource
Didesmethylcitalopram oxalateHMDB
DidesmethylcitalopramMeSH
Chemical FormulaC18H17FN2O
Average Molecular Weight296.3388
Monoisotopic Molecular Weight296.132491381
IUPAC Name1-(3-aminopropyl)-1-(4-fluorophenyl)-1,3-dihydro-2-benzofuran-5-carbonitrile
Traditional Namedidemethylcitalopram
CAS Registry NumberNot Available
SMILES
NCCCC1(OCC2=C1C=CC(=C2)C#N)C1=CC=C(F)C=C1
InChI Identifier
InChI=1S/C18H17FN2O/c19-16-5-3-15(4-6-16)18(8-1-9-20)17-7-2-13(11-21)10-14(17)12-22-18/h2-7,10H,1,8-9,12,20H2
InChI KeyRKUKMUWCRLRPEJ-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as phenylbutylamines. Phenylbutylamines are compounds containing a phenylbutylamine moiety, which consists of a phenyl group substituted at the fourth carbon by an butan-1-amine.
KingdomOrganic compounds
Super ClassBenzenoids
ClassBenzene and substituted derivatives
Sub ClassPhenylbutylamines
Direct ParentPhenylbutylamines
Alternative Parents
Substituents
  • Phenylbutylamine
  • Isocoumaran
  • Fluorobenzene
  • Halobenzene
  • Aralkylamine
  • Aryl halide
  • Aryl fluoride
  • Oxacycle
  • Dialkyl ether
  • Ether
  • Carbonitrile
  • Nitrile
  • Organoheterocyclic compound
  • Organohalogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Primary aliphatic amine
  • Amine
  • Organofluoride
  • Organonitrogen compound
  • Organooxygen compound
  • Organic nitrogen compound
  • Primary amine
  • Hydrocarbon derivative
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Ontology
Disposition

Biological location

Source

Route of exposure

Process

Naturally occurring process

Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.0052 g/LALOGPS
logP10(2.69) g/LALOGPS
logP10(2.95) g/LChemAxon
logS10(-4.8) g/LALOGPS
pKa (Strongest Basic)10.2ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area59.04 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity83.95 m³·mol⁻¹ChemAxon
Polarizability31.16 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+177.26930932474
DeepCCS[M-H]-174.91130932474

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
DidemethylcitalopramNCCCC1(OCC2=C1C=CC(=C2)C#N)C1=CC=C(F)C=C13567.9Standard polar33892256
DidemethylcitalopramNCCCC1(OCC2=C1C=CC(=C2)C#N)C1=CC=C(F)C=C12575.4Standard non polar33892256
DidemethylcitalopramNCCCC1(OCC2=C1C=CC(=C2)C#N)C1=CC=C(F)C=C12467.9Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Didemethylcitalopram,1TMS,isomer #1C[Si](C)(C)NCCCC1(C2=CC=C(F)C=C2)OCC2=CC(C#N)=CC=C212563.5Semi standard non polar33892256
Didemethylcitalopram,1TMS,isomer #1C[Si](C)(C)NCCCC1(C2=CC=C(F)C=C2)OCC2=CC(C#N)=CC=C212577.2Standard non polar33892256
Didemethylcitalopram,1TMS,isomer #1C[Si](C)(C)NCCCC1(C2=CC=C(F)C=C2)OCC2=CC(C#N)=CC=C213232.3Standard polar33892256
Didemethylcitalopram,2TMS,isomer #1C[Si](C)(C)N(CCCC1(C2=CC=C(F)C=C2)OCC2=CC(C#N)=CC=C21)[Si](C)(C)C2741.9Semi standard non polar33892256
Didemethylcitalopram,2TMS,isomer #1C[Si](C)(C)N(CCCC1(C2=CC=C(F)C=C2)OCC2=CC(C#N)=CC=C21)[Si](C)(C)C2729.4Standard non polar33892256
Didemethylcitalopram,2TMS,isomer #1C[Si](C)(C)N(CCCC1(C2=CC=C(F)C=C2)OCC2=CC(C#N)=CC=C21)[Si](C)(C)C3178.6Standard polar33892256
Didemethylcitalopram,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)NCCCC1(C2=CC=C(F)C=C2)OCC2=CC(C#N)=CC=C212832.2Semi standard non polar33892256
Didemethylcitalopram,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)NCCCC1(C2=CC=C(F)C=C2)OCC2=CC(C#N)=CC=C212781.5Standard non polar33892256
Didemethylcitalopram,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)NCCCC1(C2=CC=C(F)C=C2)OCC2=CC(C#N)=CC=C213313.7Standard polar33892256
Didemethylcitalopram,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)N(CCCC1(C2=CC=C(F)C=C2)OCC2=CC(C#N)=CC=C21)[Si](C)(C)C(C)(C)C3246.4Semi standard non polar33892256
Didemethylcitalopram,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)N(CCCC1(C2=CC=C(F)C=C2)OCC2=CC(C#N)=CC=C21)[Si](C)(C)C(C)(C)C3083.0Standard non polar33892256
Didemethylcitalopram,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)N(CCCC1(C2=CC=C(F)C=C2)OCC2=CC(C#N)=CC=C21)[Si](C)(C)C(C)(C)C3303.7Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Didemethylcitalopram GC-MS (Non-derivatized) - 70eV, Positivesplash10-0019-5190000000-27267b21fbfd2667ad0a2017-09-20Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Didemethylcitalopram GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Didemethylcitalopram GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Didemethylcitalopram 10V, Positive-QTOFsplash10-001j-0090000000-6d8ae8086154e9386c592016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Didemethylcitalopram 20V, Positive-QTOFsplash10-001i-1190000000-a3bd6197e10242280d3e2016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Didemethylcitalopram 40V, Positive-QTOFsplash10-0f6x-9850000000-29310282b6b9fbd8e49f2016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Didemethylcitalopram 10V, Negative-QTOFsplash10-0002-0090000000-b966c93238a3cd3d8dbe2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Didemethylcitalopram 20V, Negative-QTOFsplash10-0002-1090000000-6f09b8194f9dc7f22ae02016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Didemethylcitalopram 40V, Negative-QTOFsplash10-0002-5290000000-4ebf655263c971b6b6fc2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Didemethylcitalopram 10V, Positive-QTOFsplash10-0002-0090000000-1839b3c3aa4333bd08f62021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Didemethylcitalopram 20V, Positive-QTOFsplash10-0f6t-0290000000-ee8bb8dcc6c4bee4016a2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Didemethylcitalopram 40V, Positive-QTOFsplash10-0a4i-0930000000-59d6738739988f3339152021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Didemethylcitalopram 10V, Negative-QTOFsplash10-0002-0090000000-009c4b2c3fd1dd912a1c2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Didemethylcitalopram 20V, Negative-QTOFsplash10-000i-0090000000-e2f03fdefbdbf66694492021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Didemethylcitalopram 40V, Negative-QTOFsplash10-000i-1590000000-373645739048c7d4b1c22021-10-12Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
  • Membrane (predicted from logP)
Biospecimen Locations
  • Blood
  • Feces
  • Urine
Tissue Locations
  • Kidney
  • Liver
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableNormal
      Not Available
details
FecesDetected but not QuantifiedNot QuantifiedInfant (0-1 year old)Both
Normal
details
UrineExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableNormal
      Not Available
details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedNewborn (0-30 days old)Both
Sepsis
details
Associated Disorders and Diseases
Disease References
Sepsis
  1. Stewart CJ, Embleton ND, Marrs ECL, Smith DP, Fofanova T, Nelson A, Skeath T, Perry JD, Petrosino JF, Berrington JE, Cummings SP: Longitudinal development of the gut microbiome and metabolome in preterm neonates with late onset sepsis and healthy controls. Microbiome. 2017 Jul 12;5(1):75. doi: 10.1186/s40168-017-0295-1. [PubMed:28701177 ]
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDC16609
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound162976
PDB IDNot Available
ChEBI ID80604
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Magrane M: UniProt Knowledgebase: a hub of integrated protein data. Database (Oxford). 2011 Mar 29;2011:bar009. doi: 10.1093/database/bar009. Print 2011. [PubMed:21447597 ]
  2. Howland RH: A critical evaluation of the cardiac toxicity of citalopram: part 2. J Psychosoc Nurs Ment Health Serv. 2011 Dec;49(12):13-6. doi: 10.3928/02793695-20111102-04. Epub 2011 Nov 16. [PubMed:22085614 ]
  3. Rocha A, Coelho EB, Lanchote VL: Influence of quinidine, fluvoxamine, and ketoconazole on the enantioselective pharmacokinetics of citalopram in rats. Can J Physiol Pharmacol. 2008 Nov;86(11):770-6. doi: 10.1139/Y08-088. [PubMed:19011672 ]

Enzymes

General function:
Involved in oxidoreductase activity
Specific function:
Catalyzes the oxidative deamination of biogenic and xenobiotic amines and has important functions in the metabolism of neuroactive and vasoactive amines in the central nervous system and peripheral tissues. MAOB preferentially degrades benzylamine and phenylethylamine.
Gene Name:
MAOB
Uniprot ID:
P27338
Molecular weight:
58762.475
Reactions
Didemethylcitalopram + Water + Oxygen → Citalopram aldehyde + Ammonia + Hydrogen peroxidedetails
General function:
Involved in oxidoreductase activity
Specific function:
Catalyzes the oxidative deamination of biogenic and xenobiotic amines and has important functions in the metabolism of neuroactive and vasoactive amines in the central nervous system and peripheral tissues. MAOA preferentially oxidizes biogenic amines such as 5-hydroxytryptamine (5-HT), norepinephrine and epinephrine.
Gene Name:
MAOA
Uniprot ID:
P21397
Molecular weight:
59681.27
Reactions
Didemethylcitalopram + Water + Oxygen → Citalopram aldehyde + Ammonia + Hydrogen peroxidedetails