Hmdb loader
Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 22:47:18 UTC
Update Date2022-11-23 22:29:21 UTC
HMDB IDHMDB0259847
Secondary Accession NumbersNone
Metabolite Identification
Common NameVitamin D3 palmitic acid
DescriptionVitamin D3 palmitic acid, also known as vitamin D3 palmitate, belongs to the class of organic compounds known as vitamin d and derivatives. Vitamin D and derivatives are compounds containing a secosteroid backbone, usually secoergostane or secocholestane. Based on a literature review a significant number of articles have been published on Vitamin D3 palmitic acid. This compound has been identified in human blood as reported by (PMID: 31557052 ). Vitamin d3 palmitic acid is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Vitamin D3 palmitic acid 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
Thumb
Synonyms
ValueSource
Vitamin D3 palmitateGenerator
3-{2-[7a-methyl-1-(6-methylheptan-2-yl)-octahydro-1H-inden-4-ylidene]ethylidene}-4-methylidenecyclohexyl hexadecanoic acidHMDB
Vitamin D3 palmitic acidGenerator
Chemical FormulaC43H74O2
Average Molecular Weight623.063
Monoisotopic Molecular Weight622.568881623
IUPAC Name3-{2-[7a-methyl-1-(6-methylheptan-2-yl)-octahydro-1H-inden-4-ylidene]ethylidene}-4-methylidenecyclohexyl hexadecanoate
Traditional Name3-{2-[7a-methyl-1-(6-methylheptan-2-yl)-hexahydro-1H-inden-4-ylidene]ethylidene}-4-methylidenecyclohexyl hexadecanoate
CAS Registry NumberNot Available
SMILES
CCCCCCCCCCCCCCCC(=O)OC1CCC(=C)C(C1)=CC=C1CCCC2(C)C(CCC12)C(C)CCCC(C)C
InChI Identifier
InChI=1S/C43H74O2/c1-7-8-9-10-11-12-13-14-15-16-17-18-19-25-42(44)45-39-29-26-35(4)38(33-39)28-27-37-24-21-32-43(6)40(30-31-41(37)43)36(5)23-20-22-34(2)3/h27-28,34,36,39-41H,4,7-26,29-33H2,1-3,5-6H3
InChI KeyFURKZYNGFYQYCT-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as vitamin d and derivatives. Vitamin D and derivatives are compounds containing a secosteroid backbone, usually secoergostane or secocholestane.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassSteroids and steroid derivatives
Sub ClassVitamin D and derivatives
Direct ParentVitamin D and derivatives
Alternative Parents
Substituents
  • Triterpenoid
  • Fatty acid ester
  • Fatty acyl
  • Carboxylic acid ester
  • Monocarboxylic acid or derivatives
  • Carboxylic acid derivative
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Aliphatic homopolycyclic compound
Molecular FrameworkAliphatic homopolycyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
ProcessNot Available
RoleNot Available
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
logP10.71ALOGPS
logP14.05ChemAxon
logS-7.3ALOGPS
pKa (Strongest Basic)-7ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area26.3 ŲChemAxon
Rotatable Bond Count22ChemAxon
Refractivity196.82 m³·mol⁻¹ChemAxon
Polarizability83.21 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
AllCCS[M+H]+258.44732859911
AllCCS[M+H-H2O]+258.04532859911
AllCCS[M+Na]+258.88232859911
AllCCS[M+NH4]+258.78932859911
AllCCS[M-H]-214.51532859911
AllCCS[M+Na-2H]-220.3832859911
AllCCS[M+HCOO]-226.91132859911
DeepCCS[M-2H]-296.27230932474
DeepCCS[M+Na]+271.69530932474

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
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, 2022.10.14 minutes32390414
Predicted by Siyang on May 30, 202251.3065 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20221.09 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid5967.5 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid1632.9 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid600.3 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid840.1 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid1151.1 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid2328.0 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid2105.9 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)156.8 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid4572.6 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid1316.2 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid3974.6 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid1715.1 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid1080.8 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate1095.8 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA1323.1 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water10.9 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Vitamin D3 palmitateCCCCCCCCCCCCCCCC(=O)OC1CCC(=C)C(C1)=CC=C1CCCC2(C)C(CCC12)C(C)CCCC(C)C4804.7Standard polar33892256
Vitamin D3 palmitateCCCCCCCCCCCCCCCC(=O)OC1CCC(=C)C(C1)=CC=C1CCCC2(C)C(CCC12)C(C)CCCC(C)C4250.0Standard non polar33892256
Vitamin D3 palmitateCCCCCCCCCCCCCCCC(=O)OC1CCC(=C)C(C1)=CC=C1CCCC2(C)C(CCC12)C(C)CCCC(C)C4551.2Semi standard non polar33892256
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID21237115
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound76075039
PDB IDNot Available
ChEBI IDNot Available
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. 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 ]