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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 14:22:24 UTC

Update Date

2021-09-26 23:09:18 UTC

HMDB ID

HMDB0254894

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Phenanthrene-3,4-diol

Description

phenanthrene-3,4-diol, also known as 3,4-dihydroxyphenanthrene or morphol, belongs to the class of organic compounds known as phenanthrols. Phenanthrols are compounds containing a phenanthrene (or its hydrogenated derivative) to which a hydroxyl group is attached. phenanthrene-3,4-diol exists in all living organisms, ranging from bacteria to humans. phenanthrene-3,4-diol is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review very few articles have been published on phenanthrene-3,4-diol. This compound has been identified in human blood as reported by (PMID: 31557052 ). Phenanthrene-3,4-diol is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Phenanthrene-3,4-diol 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

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

 
  Mrv1533007211515382D          
 
 16 18  0  0  0  0            999 V2000
   15.0569   -7.5245    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.3756   -8.0041    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.8330   -7.9505    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.0572   -6.7321    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.3752   -8.7966    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.6407   -7.5783    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.8385   -8.7640    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.5059   -7.5486    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.8009   -6.2879    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.3789   -6.3205    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.1302   -9.1871    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.7082   -9.2196    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.9678   -7.9802    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.5147   -6.6784    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.8013   -5.4955    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.9532   -8.8292    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  2  0  0  0  0
  1  4  1  0  0  0  0
  2  5  2  0  0  0  0
  2  6  1  0  0  0  0
  3  7  1  0  0  0  0
  3  8  1  0  0  0  0
  4  9  2  0  0  0  0
  4 10  1  0  0  0  0
  5 11  1  0  0  0  0
  5 12  1  0  0  0  0
  6 13  2  0  0  0  0
  8 14  2  0  0  0  0
  9 15  1  0  0  0  0
 12 16  2  0  0  0  0
  7 11  2  0  0  0  0
  9 14  1  0  0  0  0
 13 16  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0254894

> <DATABASE_NAME>
hmdb

> <SMILES>
OC1=C(O)C2=C(C=C1)C=CC1=C2C=CC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C14H10O2/c15-12-8-7-10-6-5-9-3-1-2-4-11(9)13(10)14(12)16/h1-8,15-16H

> <INCHI_KEY>
RLZZZVKAURTHCP-UHFFFAOYSA-N

> <FORMULA>
C14H10O2

> <MOLECULAR_WEIGHT>
210.232

> <EXACT_MASS>
210.068079562

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
26

> <JCHEM_AVERAGE_POLARIZABILITY>
22.225098619869414

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
phenanthrene-3,4-diol

> <ALOGPS_LOGP>
3.33

> <JCHEM_LOGP>
3.3450686859999994

> <ALOGPS_LOGS>
-3.82

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.406028455400417

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.92683328490362

> <JCHEM_PKA_STRONGEST_BASIC>
-6.310128734403137

> <JCHEM_POLAR_SURFACE_AREA>
40.46

> <JCHEM_REFRACTIVITY>
62.92020000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.16e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
morphol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 21-JUL-15   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   21-JUL-15         0                                  
HETATM    1  C   UNK     0      28.106 -14.046   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      26.834 -14.941   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      29.555 -14.841   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      28.107 -12.567   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      26.834 -16.420   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      25.463 -14.146   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      29.565 -16.360   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      30.811 -14.091   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      29.495 -11.737   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      26.841 -11.798   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      28.243 -17.149   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      25.589 -17.210   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      24.207 -14.896   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      30.827 -12.466   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      29.496 -10.258   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      24.179 -16.481   0.000  0.00  0.00           C+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5    6                                                  
CONECT    3    1    7    8                                                  
CONECT    4    1    9   10                                                  
CONECT    5    2   11   12                                                  
CONECT    6    2   13                                                       
CONECT    7    3   11                                                       
CONECT    8    3   14                                                       
CONECT    9    4   15   14                                                  
CONECT   10    4                                                            
CONECT   11    5    7                                                       
CONECT   12    5   16                                                       
CONECT   13    6   16                                                       
CONECT   14    8    9                                                       
CONECT   15    9                                                            
CONECT   16   12   13                                                       
MASTER        0    0    0    0    0    0    0    0   16    0   36    0
END

COMPND    HMDB0254894
HETATM    1  O1  UNL     1       3.540  -1.939  -0.241  1.00  0.00           O  
HETATM    2  C1  UNL     1       2.706  -0.848  -0.024  1.00  0.00           C  
HETATM    3  C2  UNL     1       3.235   0.362   0.318  1.00  0.00           C  
HETATM    4  C3  UNL     1       2.387   1.419   0.525  1.00  0.00           C  
HETATM    5  C4  UNL     1       1.024   1.237   0.384  1.00  0.00           C  
HETATM    6  C5  UNL     1       0.155   2.290   0.589  1.00  0.00           C  
HETATM    7  C6  UNL     1      -1.199   2.151   0.459  1.00  0.00           C  
HETATM    8  C7  UNL     1      -1.743   0.922   0.111  1.00  0.00           C  
HETATM    9  C8  UNL     1      -3.109   0.789  -0.019  1.00  0.00           C  
HETATM   10  C9  UNL     1      -3.656  -0.414  -0.361  1.00  0.00           C  
HETATM   11  C10 UNL     1      -2.816  -1.507  -0.578  1.00  0.00           C  
HETATM   12  C11 UNL     1      -1.450  -1.390  -0.452  1.00  0.00           C  
HETATM   13  C12 UNL     1      -0.902  -0.179  -0.108  1.00  0.00           C  
HETATM   14  C13 UNL     1       0.468  -0.006   0.031  1.00  0.00           C  
HETATM   15  C14 UNL     1       1.318  -1.062  -0.176  1.00  0.00           C  
HETATM   16  O2  UNL     1       0.894  -2.308  -0.520  1.00  0.00           O  
HETATM   17  H1  UNL     1       4.530  -1.913  -0.165  1.00  0.00           H  
HETATM   18  H2  UNL     1       4.321   0.464   0.420  1.00  0.00           H  
HETATM   19  H3  UNL     1       2.759   2.405   0.800  1.00  0.00           H  
HETATM   20  H4  UNL     1       0.586   3.265   0.865  1.00  0.00           H  
HETATM   21  H5  UNL     1      -1.843   3.000   0.628  1.00  0.00           H  
HETATM   22  H6  UNL     1      -3.737   1.636   0.151  1.00  0.00           H  
HETATM   23  H7  UNL     1      -4.734  -0.552  -0.471  1.00  0.00           H  
HETATM   24  H8  UNL     1      -3.284  -2.453  -0.849  1.00  0.00           H  
HETATM   25  H9  UNL     1      -0.892  -2.256  -0.632  1.00  0.00           H  
HETATM   26  H10 UNL     1       1.443  -3.113  -0.684  1.00  0.00           H  
CONECT    1    2   17
CONECT    2    3    3   15
CONECT    3    4   18
CONECT    4    5    5   19
CONECT    5    6   14
CONECT    6    7    7   20
CONECT    7    8   21
CONECT    8    9    9   13
CONECT    9   10   22
CONECT   10   11   11   23
CONECT   11   12   24
CONECT   12   13   13   25
CONECT   13   14
CONECT   14   15   15
CONECT   15   16
CONECT   16   26
END

View in JSmol View Stereo Labels

Synonyms

Value	Source
3,4-Dihydroxyphenanthrene	ChEBI
3,4-Phenanthrenediol	ChEBI
Morphol	ChEBI

Chemical Formula

C₁₄H₁₀O₂

Average Molecular Weight

210.232

Monoisotopic Molecular Weight

210.068079562

IUPAC Name

phenanthrene-3,4-diol

Traditional Name

morphol

CAS Registry Number

Not Available

SMILES

OC1=C(O)C2=C(C=C1)C=CC1=C2C=CC=C1

InChI Identifier

InChI=1S/C14H10O2/c15-12-8-7-10-6-5-9-3-1-2-4-11(9)13(10)14(12)16/h1-8,15-16H

InChI Key

RLZZZVKAURTHCP-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as phenanthrols. Phenanthrols are compounds containing a phenanthrene (or its hydrogenated derivative) to which a hydroxyl group is attached.

Kingdom

Organic compounds

Super Class

Benzenoids

Class

Phenanthrenes and derivatives

Sub Class

Phenanthrols

Direct Parent

Phenanthrols

Alternative Parents

Substituents

Phenanthrol
1-naphthol
2-naphthol
Naphthalene
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Organic oxygen compound
Hydrocarbon derivative
Organooxygen compound
Aromatic homopolycyclic compound

Molecular Framework

Aromatic homopolycyclic compounds

External Descriptors

phenanthrenediol (CHEBI:16760 )
a small molecule (PHENANTHRENE-34-DIOL )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	3.33	ALOGPS
logP	3.35	ChemAxon
logS	-3.8	ALOGPS
pKa (Strongest Acidic)	8.93	ChemAxon
pKa (Strongest Basic)	-6.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	40.46 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	62.92 m³·mol⁻¹	ChemAxon
Polarizability	22.23 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M+H]+	149.746	30932474
DeepCCS	[M-H]-	147.35	30932474
DeepCCS	[M-2H]-	180.581	30932474
DeepCCS	[M+Na]+	155.658	30932474
AllCCS	[M+H]+	145.8	32859911
AllCCS	[M+H-H2O]+	141.5	32859911
AllCCS	[M+NH4]+	149.8	32859911
AllCCS	[M+Na]+	150.9	32859911
AllCCS	[M-H]-	147.4	32859911
AllCCS	[M+Na-2H]-	146.8	32859911
AllCCS	[M+HCOO]-	146.3	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Phenanthrene-3,4-diol	OC1=C(O)C2=C(C=C1)C=CC1=C2C=CC=C1	3615.9	Standard polar	33892256
Phenanthrene-3,4-diol	OC1=C(O)C2=C(C=C1)C=CC1=C2C=CC=C1	2252.8	Standard non polar	33892256
Phenanthrene-3,4-diol	OC1=C(O)C2=C(C=C1)C=CC1=C2C=CC=C1	2331.8	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Phenanthrene-3,4-diol GC-MS (Non-derivatized) - 70eV, Positive	splash10-01q9-0920000000-45e8564a8370ae84d686	2021-09-23	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Phenanthrene-3,4-diol GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Phenanthrene-3,4-diol GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Phenanthrene-3,4-diol GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Phenanthrene-3,4-diol GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Phenanthrene-3,4-diol GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Phenanthrene-3,4-diol GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Phenanthrene-3,4-diol GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Phenanthrene-3,4-diol 10V, Positive-QTOF	splash10-03di-0090000000-3bc471ce6decb92c8cfb	2019-02-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Phenanthrene-3,4-diol 20V, Positive-QTOF	splash10-03di-0490000000-8ee2c9fb5e2073eda1e6	2019-02-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Phenanthrene-3,4-diol 40V, Positive-QTOF	splash10-0udi-0900000000-793ef7af803cfa0c80a5	2019-02-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Phenanthrene-3,4-diol 10V, Negative-QTOF	splash10-0a4i-0090000000-50f87ca7aa27395f9ca7	2019-02-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Phenanthrene-3,4-diol 20V, Negative-QTOF	splash10-0a4i-0090000000-2d6b67fc2a91e7a0eb19	2019-02-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Phenanthrene-3,4-diol 40V, Negative-QTOF	splash10-0zgi-0920000000-2c1aa71d78594c31f501	2019-02-23	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	31557052	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

388959

KEGG Compound ID

C03164

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

16760

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

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 ]

Showing metabocard for Phenanthrene-3,4-diol (HMDB0254894)

MOL for HMDB0254894 (Phenanthrene-3,4-diol)

3D MOL for HMDB0254894 (Phenanthrene-3,4-diol)

3D SDF for HMDB0254894 (Phenanthrene-3,4-diol)

3D-SDF for HMDB0254894 (Phenanthrene-3,4-diol)

PDB for HMDB0254894 (Phenanthrene-3,4-diol)

3D PDB for HMDB0254894 (Phenanthrene-3,4-diol)

SMILES for HMDB0254894 (Phenanthrene-3,4-diol)

INCHI for HMDB0254894 (Phenanthrene-3,4-diol)

Structure for HMDB0254894 (Phenanthrene-3,4-diol)

3D Structure for HMDB0254894 (Phenanthrene-3,4-diol)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra