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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 00:36:26 UTC

Update Date

2021-09-26 22:57:23 UTC

HMDB ID

HMDB0247604

Secondary Accession Numbers

None

Metabolite Identification

Common Name

9-Nitrophenanthrene

Description

9-Nitrophenanthrene belongs to the class of organic compounds known as phenanthrenes and derivatives. These are polycyclic compounds containing a phenanthrene moiety, which is a tricyclic aromatic compound with three non-linearly fused benzene. Based on a literature review very few articles have been published on 9-Nitrophenanthrene. This compound has been identified in human blood as reported by (PMID: 31557052 ). 9-nitrophenanthrene is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 9-Nitrophenanthrene 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


  Mrv1572004191602202D          

 17 19  0  0  0  0            999 V2000
    4.7289    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3164    2.3645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0164    2.3645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6039    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3164    0.9355    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4914    2.3645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8414    2.3645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0164    0.9355    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0789    0.2211    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4914    0.9355    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0789    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8414    0.9355    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539    0.2211    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8414   -0.4934    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0164   -0.4934    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539   -1.2079    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  4  3  2  0  0  0  0
  5  1  1  0  0  0  0
  6  2  1  0  0  0  0
  7  3  1  0  0  0  0
  8  4  1  0  0  0  0
 10  5  2  0  0  0  0
 10  9  1  0  0  0  0
 11  6  2  0  0  0  0
 11 10  1  0  0  0  0
 12  7  2  0  0  0  0
 12 11  1  0  0  0  0
 13  8  2  0  0  0  0
 13 12  1  0  0  0  0
 14  9  2  0  0  0  0
 14 13  1  0  0  0  0
 15 14  1  0  0  0  0
 16 15  2  0  0  0  0
 17 15  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0247604

> <DATABASE_NAME>
hmdb

> <SMILES>
O=N(=O)C1=CC2=CC=CC=C2C2=CC=CC=C12

> <INCHI_IDENTIFIER>
InChI=1S/C14H9NO2/c16-15(17)14-9-10-5-1-2-6-11(10)12-7-3-4-8-13(12)14/h1-9H

> <INCHI_KEY>
QTTCNQHPKFAYEZ-UHFFFAOYSA-N

> <FORMULA>
C14H9NO2

> <MOLECULAR_WEIGHT>
223.231

> <EXACT_MASS>
223.063328534

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
26

> <JCHEM_AVERAGE_POLARIZABILITY>
22.814211404296916

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
9-nitrophenanthrene

> <ALOGPS_LOGP>
4.62

> <JCHEM_LOGP>
3.8921835186666662

> <ALOGPS_LOGS>
-5.20

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
45.82

> <JCHEM_REFRACTIVITY>
66.2831

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.42e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
9-nitrophenanthrene

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 19-APR-16   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-APR-16         0                                  
HETATM    1  C   UNK     0       8.827   3.080   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       8.057   4.414   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.897   4.414   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.127   3.080   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.057   1.746   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.517   4.414   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.437   4.414   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.897   1.746   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.747   0.413   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.517   1.746   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.747   3.080   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.207   3.080   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       3.437   1.746   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.207   0.413   0.000  0.00  0.00           C+0
HETATM   15  N   UNK     0       3.437  -0.921   0.000  0.00  0.00           N+0
HETATM   16  O   UNK     0       1.897  -0.921   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       4.207  -2.255   0.000  0.00  0.00           O+0
CONECT    1    2    5                                                       
CONECT    2    1    6                                                       
CONECT    3    4    7                                                       
CONECT    4    3    8                                                       
CONECT    5    1   10                                                       
CONECT    6    2   11                                                       
CONECT    7    3   12                                                       
CONECT    8    4   13                                                       
CONECT    9   10   14                                                       
CONECT   10    5    9   11                                                  
CONECT   11    6   10   12                                                  
CONECT   12    7   11   13                                                  
CONECT   13    8   12   14                                                  
CONECT   14    9   13   15                                                  
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   38    0
END

COMPND    HMDB0247604
HETATM    1  O1  UNL     1      -2.874   2.833  -0.169  1.00  0.00           O  
HETATM    2  N1  UNL     1      -1.771   2.754   0.354  1.00  0.00           N1+
HETATM    3  O2  UNL     1      -1.373   3.861   1.108  1.00  0.00           O1-
HETATM    4  C1  UNL     1      -0.900   1.661   0.197  1.00  0.00           C  
HETATM    5  C2  UNL     1       0.487   1.887   0.126  1.00  0.00           C  
HETATM    6  C3  UNL     1       1.391   0.867  -0.024  1.00  0.00           C  
HETATM    7  C4  UNL     1       2.748   1.105  -0.094  1.00  0.00           C  
HETATM    8  C5  UNL     1       3.646   0.089  -0.245  1.00  0.00           C  
HETATM    9  C6  UNL     1       3.197  -1.205  -0.330  1.00  0.00           C  
HETATM   10  C7  UNL     1       1.824  -1.468  -0.261  1.00  0.00           C  
HETATM   11  C8  UNL     1       0.923  -0.441  -0.109  1.00  0.00           C  
HETATM   12  C9  UNL     1      -0.446  -0.722  -0.043  1.00  0.00           C  
HETATM   13  C10 UNL     1      -0.922  -2.006  -0.116  1.00  0.00           C  
HETATM   14  C11 UNL     1      -2.264  -2.303  -0.042  1.00  0.00           C  
HETATM   15  C12 UNL     1      -3.127  -1.256   0.109  1.00  0.00           C  
HETATM   16  C13 UNL     1      -2.684   0.045   0.185  1.00  0.00           C  
HETATM   17  C14 UNL     1      -1.341   0.357   0.112  1.00  0.00           C  
HETATM   18  H1  UNL     1       0.854   2.902   0.193  1.00  0.00           H  
HETATM   19  H2  UNL     1       3.069   2.114  -0.024  1.00  0.00           H  
HETATM   20  H3  UNL     1       4.721   0.236  -0.304  1.00  0.00           H  
HETATM   21  H4  UNL     1       3.870  -2.019  -0.449  1.00  0.00           H  
HETATM   22  H5  UNL     1       1.489  -2.479  -0.331  1.00  0.00           H  
HETATM   23  H6  UNL     1      -0.281  -2.860  -0.235  1.00  0.00           H  
HETATM   24  H7  UNL     1      -2.631  -3.340  -0.102  1.00  0.00           H  
HETATM   25  H8  UNL     1      -4.188  -1.464   0.169  1.00  0.00           H  
HETATM   26  H9  UNL     1      -3.417   0.852   0.324  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    4    5    5   17
CONECT    5    6   18
CONECT    6    7    7   11
CONECT    7    8   19
CONECT    8    9    9   20
CONECT    9   10   21
CONECT   10   11   11   22
CONECT   11   12
CONECT   12   13   13   17
CONECT   13   14   23
CONECT   14   15   15   24
CONECT   15   16   25
CONECT   16   17   17   26
END

View in JSmol View Stereo Labels

Synonyms

Value	Source
9-nitro-Phenanthrene	ChEMBL

Chemical Formula

C₁₄H₉NO₂

Average Molecular Weight

223.231

Monoisotopic Molecular Weight

223.063328534

IUPAC Name

9-nitrophenanthrene

Traditional Name

9-nitrophenanthrene

CAS Registry Number

Not Available

SMILES

O=N(=O)C1=CC2=CC=CC=C2C2=CC=CC=C12

InChI Identifier

InChI=1S/C14H9NO2/c16-15(17)14-9-10-5-1-2-6-11(10)12-7-3-4-8-13(12)14/h1-9H

InChI Key

QTTCNQHPKFAYEZ-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as phenanthrenes and derivatives. These are polycyclic compounds containing a phenanthrene moiety, which is a tricyclic aromatic compound with three non-linearly fused benzene.

Kingdom

Organic compounds

Super Class

Benzenoids

Class

Phenanthrenes and derivatives

Sub Class

Not Available

Direct Parent

Phenanthrenes and derivatives

Alternative Parents

Substituents

Phenanthrene
1-nitronaphthalene
2-nitronaphthalene
Naphthalene
Nitroaromatic compound
C-nitro compound
Organic nitro compound
Organic oxoazanium
Allyl-type 1,3-dipolar organic compound
Propargyl-type 1,3-dipolar organic compound
Organic 1,3-dipolar compound
Organonitrogen compound
Organic oxide
Hydrocarbon derivative
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Aromatic homopolycyclic compound

Molecular Framework

Aromatic homopolycyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Source

Exogenous

Exogenous (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	4.62	ALOGPS
logP	3.89	ChemAxon
logS	-5.2	ALOGPS
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	45.82 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	66.28 m³·mol⁻¹	ChemAxon
Polarizability	22.81 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-2H]-	175.277	30932474
DeepCCS	[M+Na]+	150.195	30932474
AllCCS	[M+H]+	146.7	32859911
AllCCS	[M+H-H2O]+	142.5	32859911
AllCCS	[M+NH4]+	150.6	32859911
AllCCS	[M+Na]+	151.7	32859911
AllCCS	[M-H]-	147.0	32859911
AllCCS	[M+Na-2H]-	146.0	32859911
AllCCS	[M+HCOO]-	144.9	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
9-Nitrophenanthrene	O=N(=O)C1=CC2=CC=CC=C2C2=CC=CC=C12	3243.8	Standard polar	33892256
9-Nitrophenanthrene	O=N(=O)C1=CC2=CC=CC=C2C2=CC=CC=C12	2127.2	Standard non polar	33892256
9-Nitrophenanthrene	O=N(=O)C1=CC2=CC=CC=C2C2=CC=CC=C12	2212.3	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 - 9-Nitrophenanthrene GC-MS (Non-derivatized) - 70eV, Positive	splash10-00di-0490000000-9212ca6bf4960f9c6654	2021-09-23	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 9-Nitrophenanthrene GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	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 - 9-Nitrophenanthrene 10V, Positive-QTOF	splash10-00di-0090000000-457f289209ef62c61c11	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 9-Nitrophenanthrene 20V, Positive-QTOF	splash10-00di-0090000000-c004602fae57686431d6	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 9-Nitrophenanthrene 40V, Positive-QTOF	splash10-00di-1390000000-2e234af500c40b7e12db	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 9-Nitrophenanthrene 10V, Negative-QTOF	splash10-00di-0090000000-6f37aae4e8428ca735e2	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 9-Nitrophenanthrene 20V, Negative-QTOF	splash10-00di-0090000000-2c6b6a8db22f14e2dca5	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 9-Nitrophenanthrene 40V, Negative-QTOF	splash10-00di-1190000000-3c51d5c808d0ab27109c	2016-08-03	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

63563

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

70382

PDB ID

Not Available

ChEBI ID

Not Available

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 9-Nitrophenanthrene (HMDB0247604)

MOL for HMDB0247604 (9-Nitrophenanthrene)

3D MOL for HMDB0247604 (9-Nitrophenanthrene)

3D SDF for HMDB0247604 (9-Nitrophenanthrene)

3D-SDF for HMDB0247604 (9-Nitrophenanthrene)

PDB for HMDB0247604 (9-Nitrophenanthrene)

3D PDB for HMDB0247604 (9-Nitrophenanthrene)

SMILES for HMDB0247604 (9-Nitrophenanthrene)

INCHI for HMDB0247604 (9-Nitrophenanthrene)

Structure for HMDB0247604 (9-Nitrophenanthrene)

3D Structure for HMDB0247604 (9-Nitrophenanthrene)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra