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Showing metabocard for Propylene carbonate (HMDB0256840)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 17:26:00 UTC
Update Date2021-09-26 23:12:48 UTC
HMDB IDHMDB0256840
Secondary Accession NumbersNone
Metabolite Identification
Common NamePropylene carbonate
Description4-methyl-1,3-dioxolan-2-one belongs to the class of organic compounds known as carbonic acid diesters. Carbonic acid diesters are compounds comprising the carbonic acid diester functional group. Based on a literature review very few articles have been published on 4-methyl-1,3-dioxolan-2-one. This compound has been identified in human blood as reported by (PMID: 31557052 ). Propylene carbonate is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Propylene carbonate 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
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0256840 (Propylene carbonate)


  Mrv1652304051723392D          

  7  7  0  0  0  0            999 V2000
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
  2  7  1  0  0  0  0
M  END
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3D MOL for HMDB0256840 (Propylene carbonate)

HMDB0256840
     RDKit          3D
Propylene carbonate
 13 13  0  0  0  0  0  0  0  0999 V2000
    1.5060    0.4118    0.2845 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3293    0.0667   -0.6151 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4138   -1.0596    0.0557 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7590   -0.6537    0.1141 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7847    0.7419   -0.0269 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7703    1.4388    0.3377 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5994    1.1320   -0.5996 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0623    0.7757    1.2384 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0311   -0.5510    0.4788 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1817    1.1409   -0.1848 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6495   -0.2184   -1.6195 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3679   -1.9812   -0.5613 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0649   -1.2438    1.0979 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  7  2  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  0
  3 12  1  0
  3 13  1  0
M  END
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3D SDF for HMDB0256840 (Propylene carbonate)


  Mrv1652304051723392D          

  7  7  0  0  0  0            999 V2000
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
  2  7  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0256840

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1COC(=O)O1

> <INCHI_IDENTIFIER>
InChI=1S/C4H6O3/c1-3-2-6-4(5)7-3/h3H,2H2,1H3

> <INCHI_KEY>
RUOJZAUFBMNUDX-UHFFFAOYSA-N

> <FORMULA>
C4H6O3

> <MOLECULAR_WEIGHT>
102.089

> <EXACT_MASS>
102.031694053

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
13

> <JCHEM_AVERAGE_POLARIZABILITY>
9.119581139759138

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-methyl-1,3-dioxolan-2-one

> <ALOGPS_LOGP>
0.13

> <JCHEM_LOGP>
0.786889559

> <ALOGPS_LOGS>
0.52

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-5.5673344457229

> <JCHEM_POLAR_SURFACE_AREA>
35.53

> <JCHEM_REFRACTIVITY>
21.486200000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.38e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
propylene carbonate

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0256840 (Propylene carbonate)

HMDB0256840
     RDKit          3D
Propylene carbonate
 13 13  0  0  0  0  0  0  0  0999 V2000
    1.5060    0.4118    0.2845 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3293    0.0667   -0.6151 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4138   -1.0596    0.0557 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7590   -0.6537    0.1141 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7847    0.7419   -0.0269 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7703    1.4388    0.3377 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5994    1.1320   -0.5996 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0623    0.7757    1.2384 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0311   -0.5510    0.4788 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1817    1.1409   -0.1848 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6495   -0.2184   -1.6195 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3679   -1.9812   -0.5613 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0649   -1.2438    1.0979 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  7  2  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  0
  3 12  1  0
  3 13  1  0
M  END
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PDB for HMDB0256840 (Propylene carbonate)

HEADER    PROTEIN                                 05-APR-17   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-APR-17         0                                  
HETATM    1  C   UNK     0       1.060   3.620   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       1.830  -0.290   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -0.615  -1.536   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      -0.186   1.175   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    2                                                       
MASTER        0    0    0    0    0    0    0    0    7    0   14    0
END
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3D PDB for HMDB0256840 (Propylene carbonate)

COMPND    HMDB0256840
HETATM    1  C1  UNL     1       1.506   0.412   0.285  1.00  0.00           C  
HETATM    2  C2  UNL     1       0.329   0.067  -0.615  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.414  -1.060   0.056  1.00  0.00           C  
HETATM    4  O1  UNL     1      -1.759  -0.654   0.114  1.00  0.00           O  
HETATM    5  C4  UNL     1      -1.785   0.742  -0.027  1.00  0.00           C  
HETATM    6  O2  UNL     1      -2.770   1.439   0.338  1.00  0.00           O  
HETATM    7  O3  UNL     1      -0.599   1.132  -0.600  1.00  0.00           O  
HETATM    8  H1  UNL     1       1.062   0.776   1.238  1.00  0.00           H  
HETATM    9  H2  UNL     1       2.031  -0.551   0.479  1.00  0.00           H  
HETATM   10  H3  UNL     1       2.182   1.141  -0.185  1.00  0.00           H  
HETATM   11  H4  UNL     1       0.650  -0.218  -1.619  1.00  0.00           H  
HETATM   12  H5  UNL     1      -0.368  -1.981  -0.561  1.00  0.00           H  
HETATM   13  H6  UNL     1      -0.065  -1.244   1.098  1.00  0.00           H  
CONECT    1    2    8    9   10
CONECT    2    3    7   11
CONECT    3    4   12   13
CONECT    4    5
CONECT    5    6    6    7
END
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SMILES for HMDB0256840 (Propylene carbonate)

CC1COC(=O)O1
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INCHI for HMDB0256840 (Propylene carbonate)

InChI=1S/C4H6O3/c1-3-2-6-4(5)7-3/h3H,2H2,1H3
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View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC4H6O3
Average Molecular Weight102.089
Monoisotopic Molecular Weight102.031694053
IUPAC Name4-methyl-1,3-dioxolan-2-one
Traditional Namepropylene carbonate
CAS Registry NumberNot Available
SMILES
CC1COC(=O)O1
InChI Identifier
InChI=1S/C4H6O3/c1-3-2-6-4(5)7-3/h3H,2H2,1H3
InChI KeyRUOJZAUFBMNUDX-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as carbonic acid diesters. Carbonic acid diesters are compounds comprising the carbonic acid diester functional group.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassOrganic carbonic acids and derivatives
Sub ClassCarbonic acid diesters
Direct ParentCarbonic acid diesters
Alternative Parents
Substituents
  • Carbonic acid diester
  • Meta-dioxolane
  • Oxacycle
  • Organoheterocyclic compound
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
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
logP0.13ALOGPS
logP0.79ChemAxon
logS0.52ALOGPS
pKa (Strongest Basic)-5.6ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area35.53 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity21.49 m³·mol⁻¹ChemAxon
Polarizability9.12 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+127.05630932474
DeepCCS[M-H]-125.02430932474
DeepCCS[M-2H]-160.91630932474
DeepCCS[M+Na]+135.32330932474
AllCCS[M+H]+122.032859911
AllCCS[M+H-H2O]+117.032859911
AllCCS[M+NH4]+126.632859911
AllCCS[M+Na]+128.032859911
AllCCS[M-H]-119.232859911
AllCCS[M+Na-2H]-122.432859911
AllCCS[M+HCOO]-125.932859911

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, 2022.3.65 minutes32390414
Predicted by Siyang on May 30, 202212.0586 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20222.57 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1697.2 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid445.0 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid171.1 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid313.2 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid162.0 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid424.8 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 Acid627.6 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)153.1 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid900.8 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid322.7 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1152.2 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid316.0 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid379.2 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate669.6 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA456.3 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water171.5 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Propylene carbonateCC1COC(=O)O11757.1Standard polar33892256
Propylene carbonateCC1COC(=O)O1854.7Standard non polar33892256
Propylene carbonateCC1COC(=O)O11051.0Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Propylene carbonate GC-MS (Non-derivatized) - 70eV, Positivesplash10-054o-9000000000-b6599976fe57c5ae548f2021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Propylene carbonate GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
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 ID7636
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1040401
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 ]