Hmdb loader

Showing metabocard for 2H-Chromene (HMDB0245762)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-10 22:48:56 UTC
Update Date2021-09-26 22:54:25 UTC
HMDB IDHMDB0245762
Secondary Accession NumbersNone
Metabolite Identification
Common Name2H-Chromene
Description2H-Chromene, also known as 1,2-benzopyran or chromene I, belongs to the class of organic compounds known as 1-benzopyrans. These are organic aromatic compounds that 1-benzopyran, a bicyclic compound made up of a benzene ring fused to a pyran, so that the oxygen atom is at the 1-position. Based on a literature review a significant number of articles have been published on 2H-Chromene. This compound has been identified in human blood as reported by (PMID: 31557052 ). 2h-chromene is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 2H-Chromene 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
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0245762 (2H-Chromene)


  Mrv1652309112100492D          

 10 11  0  0  0  0            999 V2000
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  4  9  1  0  0  0  0
  9 10  1  0  0  0  0
  1 10  1  0  0  0  0
M  END
Download

3D MOL for HMDB0245762 (2H-Chromene)

HMDB0245762
     RDKit          3D
2H-Chromene
 18 19  0  0  0  0  0  0  0  0999 V2000
   -2.3320   -0.6145    0.0393 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2039   -1.2288    0.3366 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0827   -0.5635    0.2050 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2797   -1.2003    0.5153 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5065   -0.5849    0.3964 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5323    0.7184   -0.0507 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3462    1.3587   -0.3614 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1159    0.7393   -0.2414 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0705    1.3581   -0.5447 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3532    0.7854   -0.4447 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3086   -1.0926    0.1299 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2355   -2.2343    0.6807 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2119   -2.2212    0.8620 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4257   -1.0923    0.6410 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4788    1.2373   -0.1577 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3392    2.3753   -0.7122 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0171    1.4112    0.1861 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7983    0.8487   -1.4796 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  1  0
 10  1  1  0
  8  3  1  0
  1 11  1  0
  2 12  1  0
  4 13  1  0
  5 14  1  0
  6 15  1  0
  7 16  1  0
 10 17  1  0
 10 18  1  0
M  END
Download

3D SDF for HMDB0245762 (2H-Chromene)


  Mrv1652309112100492D          

 10 11  0  0  0  0            999 V2000
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  4  9  1  0  0  0  0
  9 10  1  0  0  0  0
  1 10  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0245762

> <DATABASE_NAME>
hmdb

> <SMILES>
C1OC2=CC=CC=C2C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C9H8O/c1-2-6-9-8(4-1)5-3-7-10-9/h1-6H,7H2

> <INCHI_KEY>
KYNSBQPICQTCGU-UHFFFAOYSA-N

> <FORMULA>
C9H8O

> <MOLECULAR_WEIGHT>
132.162

> <EXACT_MASS>
132.057514878

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
14.201228716524867

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2H-chromene

> <ALOGPS_LOGP>
2.29

> <JCHEM_LOGP>
2.176717525

> <ALOGPS_LOGS>
-2.41

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-4.875301691050664

> <JCHEM_POLAR_SURFACE_AREA>
9.23

> <JCHEM_REFRACTIVITY>
41.394400000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.19e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2H-1-benzopyran

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0245762 (2H-Chromene)

HMDB0245762
     RDKit          3D
2H-Chromene
 18 19  0  0  0  0  0  0  0  0999 V2000
   -2.3320   -0.6145    0.0393 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2039   -1.2288    0.3366 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0827   -0.5635    0.2050 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2797   -1.2003    0.5153 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5065   -0.5849    0.3964 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5323    0.7184   -0.0507 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3462    1.3587   -0.3614 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1159    0.7393   -0.2414 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0705    1.3581   -0.5447 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3532    0.7854   -0.4447 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3086   -1.0926    0.1299 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2355   -2.2343    0.6807 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2119   -2.2212    0.8620 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4257   -1.0923    0.6410 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4788    1.2373   -0.1577 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3392    2.3753   -0.7122 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0171    1.4112    0.1861 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7983    0.8487   -1.4796 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  1  0
 10  1  1  0
  8  3  1  0
  1 11  1  0
  2 12  1  0
  4 13  1  0
  5 14  1  0
  6 15  1  0
  7 16  1  0
 10 17  1  0
 10 18  1  0
M  END
Download

PDB for HMDB0245762 (2H-Chromene)

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       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       2.667  -3.080   0.000  0.00  0.00           O+0
CONECT    1    2   10                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5    9                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8    4   10                                                  
CONECT   10    9    1                                                       
MASTER        0    0    0    0    0    0    0    0   10    0   22    0
END
Download

3D PDB for HMDB0245762 (2H-Chromene)

COMPND    HMDB0245762
HETATM    1  C1  UNL     1      -2.332  -0.614   0.039  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.204  -1.229   0.337  1.00  0.00           C  
HETATM    3  C3  UNL     1       0.083  -0.564   0.205  1.00  0.00           C  
HETATM    4  C4  UNL     1       1.280  -1.200   0.515  1.00  0.00           C  
HETATM    5  C5  UNL     1       2.506  -0.585   0.396  1.00  0.00           C  
HETATM    6  C6  UNL     1       2.532   0.718  -0.051  1.00  0.00           C  
HETATM    7  C7  UNL     1       1.346   1.359  -0.361  1.00  0.00           C  
HETATM    8  C8  UNL     1       0.116   0.739  -0.241  1.00  0.00           C  
HETATM    9  O1  UNL     1      -1.071   1.358  -0.545  1.00  0.00           O  
HETATM   10  C9  UNL     1      -2.353   0.785  -0.445  1.00  0.00           C  
HETATM   11  H1  UNL     1      -3.309  -1.093   0.130  1.00  0.00           H  
HETATM   12  H2  UNL     1      -1.235  -2.234   0.681  1.00  0.00           H  
HETATM   13  H3  UNL     1       1.212  -2.221   0.862  1.00  0.00           H  
HETATM   14  H4  UNL     1       3.426  -1.092   0.641  1.00  0.00           H  
HETATM   15  H5  UNL     1       3.479   1.237  -0.158  1.00  0.00           H  
HETATM   16  H6  UNL     1       1.339   2.375  -0.712  1.00  0.00           H  
HETATM   17  H7  UNL     1      -3.017   1.411   0.186  1.00  0.00           H  
HETATM   18  H8  UNL     1      -2.798   0.849  -1.480  1.00  0.00           H  
CONECT    1    2    2   10   11
CONECT    2    3   12
CONECT    3    4    4    8
CONECT    4    5   13
CONECT    5    6    6   14
CONECT    6    7   15
CONECT    7    8    8   16
CONECT    8    9
CONECT    9   10
CONECT   10   17   18
END
Download

SMILES for HMDB0245762 (2H-Chromene)

C1OC2=CC=CC=C2C=C1
Download

INCHI for HMDB0245762 (2H-Chromene)

InChI=1S/C9H8O/c1-2-6-9-8(4-1)5-3-7-10-9/h1-6H,7H2
Download
View in JSmolView Stereo Labels
Synonyms
ValueSource
1,2-BenzopyranChEBI
2H-1-BenzopyranChEBI
3-ChromeneChEBI
Delta-3-ChromeneChEBI
Δ-3-chromeneGenerator
5,7-Dimethoxy-2-methyl-2H-benzopyranHMDB
Chromene IHMDB
Chemical FormulaC9H8O
Average Molecular Weight132.162
Monoisotopic Molecular Weight132.057514878
IUPAC Name2H-chromene
Traditional Name2H-1-benzopyran
CAS Registry NumberNot Available
SMILES
C1OC2=CC=CC=C2C=C1
InChI Identifier
InChI=1S/C9H8O/c1-2-6-9-8(4-1)5-3-7-10-9/h1-6H,7H2
InChI KeyKYNSBQPICQTCGU-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as 1-benzopyrans. These are organic aromatic compounds that 1-benzopyran, a bicyclic compound made up of a benzene ring fused to a pyran, so that the oxygen atom is at the 1-position.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassBenzopyrans
Sub Class1-benzopyrans
Direct Parent1-benzopyrans
Alternative Parents
Substituents
  • 1-benzopyran
  • Alkyl aryl ether
  • Benzenoid
  • Oxacycle
  • Ether
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Organooxygen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological location
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
logP2.29ALOGPS
logP2.18ChemAxon
logS-2.4ALOGPS
pKa (Strongest Basic)-4.9ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area9.23 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity41.39 m³·mol⁻¹ChemAxon
Polarizability14.2 ųChemAxon
Number of Rings2ChemAxon
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]+128.39130932474
DeepCCS[M-H]-125.32730932474
DeepCCS[M-2H]-162.21730932474
DeepCCS[M+Na]+137.49830932474
AllCCS[M+H]+124.832859911
AllCCS[M+H-H2O]+119.732859911
AllCCS[M+NH4]+129.532859911
AllCCS[M+Na]+130.832859911
AllCCS[M-H]-123.732859911
AllCCS[M+Na-2H]-124.832859911
AllCCS[M+HCOO]-126.032859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
2H-ChromeneC1OC2=CC=CC=C2C=C11617.8Standard polar33892256
2H-ChromeneC1OC2=CC=CC=C2C=C11153.3Standard non polar33892256
2H-ChromeneC1OC2=CC=CC=C2C=C11189.5Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 2H-Chromene GC-MS (Non-derivatized) - 70eV, Positivesplash10-0kai-1900000000-25afd07562dfed9b0d212021-09-24Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2H-Chromene 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 - 2H-Chromene 10V, Positive-QTOFsplash10-001i-0900000000-36daeb4f59cd49517f072021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2H-Chromene 20V, Positive-QTOFsplash10-001i-1900000000-f76dd5320ee23eaddf3d2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2H-Chromene 40V, Positive-QTOFsplash10-02t9-9400000000-1886553314b46c69bc5d2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2H-Chromene 10V, Negative-QTOFsplash10-001i-0900000000-c0c4b3e04b2d5dbfb7252021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2H-Chromene 20V, Negative-QTOFsplash10-001i-0900000000-b124559c0417b86691262021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2H-Chromene 40V, Negative-QTOFsplash10-003r-0900000000-8658482514a7b011c11e2021-10-12Wishart 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 IDC00055764
Chemspider ID8856
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound9211
PDB IDNot Available
ChEBI ID35601
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 ]