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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-24 10:17:30 UTC

Update Date

2022-09-22 18:34:38 UTC

HMDB ID

HMDB0304504

Secondary Accession Numbers

None

Metabolite Identification

Common Name

trans-3'-hydroxycotinine

Description

Trans-3'-hydroxycotinine, also known as 1-methyl-3-hydroxy-5-(3-pyridyl)-2-pyrrolidinone, is a member of the class of compounds known as pyrrolidinylpyridines. Pyrrolidinylpyridines are compounds containing a pyrrolidinylpyridine ring system, which consists of a pyrrolidine ring linked to a pyridine ring. Trans-3'-hydroxycotinine is soluble (in water) and a very weakly acidic compound (based on its pKa). Trans-3'-hydroxycotinine can be found in a number of food items such as annual wild rice, macadamia nut, corn salad, and radish, which makes trans-3'-hydroxycotinine a potential biomarker for the consumption of these food products.

Structure

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


  Mrv1533004171521122D          

 14 15  0  0  0  0            999 V2000
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3819   -1.7224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270   -2.5070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020   -2.5070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1830   -3.1745    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0470   -1.7224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7376   -1.4675    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1665   -1.4675    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3381   -0.6605    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1227   -0.4056    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7358   -0.9576    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5642   -1.7646    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.7796   -2.0195    0.0000 C   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  1  0  0  0  0
  5  7  1  0  0  0  0
  2  7  1  0  0  0  0
  7  8  2  0  0  0  0
  3  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
  9 14  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0304504

> <DATABASE_NAME>
hmdb

> <SMILES>
CN1C(CC(O)C1=O)C1=CC=CN=C1

> <INCHI_IDENTIFIER>
InChI=1S/C10H12N2O2/c1-12-8(5-9(13)10(12)14)7-3-2-4-11-6-7/h2-4,6,8-9,13H,5H2,1H3

> <INCHI_KEY>
XOKCJXZZNAUIQN-UHFFFAOYSA-N

> <FORMULA>
C10H12N2O2

> <MOLECULAR_WEIGHT>
192.218

> <EXACT_MASS>
192.089877634

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
26

> <JCHEM_AVERAGE_POLARIZABILITY>
19.506098262654007

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-hydroxy-1-methyl-5-(pyridin-3-yl)pyrrolidin-2-one

> <ALOGPS_LOGP>
-0.32

> <JCHEM_LOGP>
-0.7332253989999996

> <ALOGPS_LOGS>
-0.61

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.107323140437018

> <JCHEM_PKA_STRONGEST_BASIC>
4.788748646548031

> <JCHEM_POLAR_SURFACE_AREA>
53.43

> <JCHEM_REFRACTIVITY>
50.7291

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.77e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-hydroxy-1-methyl-5-(pyridin-3-yl)pyrrolidin-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-APR-15         0                                  
HETATM    1  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       1.334  -2.310   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0       2.580  -3.215   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.104  -4.680   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.564  -4.680   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -0.342  -5.926   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       0.088  -3.215   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -1.377  -2.739   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       4.044  -2.739   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.364  -1.233   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.829  -0.757   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.973  -1.788   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0       6.653  -3.294   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0       5.189  -3.770   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4    9                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    2    8                                                  
CONECT    8    7                                                            
CONECT    9    3   10   14                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13    9                                                       
MASTER        0    0    0    0    0    0    0    0   14    0   30    0
END

COMPND    HMDB0304504
HETATM    1  C1  UNL     1      -1.359   2.176  -0.128  1.00  0.00           C  
HETATM    2  N1  UNL     1      -1.274   0.754   0.090  1.00  0.00           N  
HETATM    3  C2  UNL     1      -2.037   0.019   1.039  1.00  0.00           C  
HETATM    4  O1  UNL     1      -2.595   0.482   2.063  1.00  0.00           O  
HETATM    5  C3  UNL     1      -2.077  -1.429   0.620  1.00  0.00           C  
HETATM    6  O2  UNL     1      -3.148  -1.564  -0.289  1.00  0.00           O  
HETATM    7  C4  UNL     1      -0.812  -1.550  -0.165  1.00  0.00           C  
HETATM    8  C5  UNL     1      -0.422  -0.168  -0.594  1.00  0.00           C  
HETATM    9  C6  UNL     1       1.020   0.021  -0.270  1.00  0.00           C  
HETATM   10  C7  UNL     1       1.991   0.022  -1.251  1.00  0.00           C  
HETATM   11  C8  UNL     1       3.336   0.196  -0.973  1.00  0.00           C  
HETATM   12  C9  UNL     1       3.706   0.376   0.357  1.00  0.00           C  
HETATM   13  N2  UNL     1       2.768   0.378   1.325  1.00  0.00           N  
HETATM   14  C10 UNL     1       1.449   0.205   1.030  1.00  0.00           C  
HETATM   15  H1  UNL     1      -1.389   2.374  -1.227  1.00  0.00           H  
HETATM   16  H2  UNL     1      -0.551   2.746   0.381  1.00  0.00           H  
HETATM   17  H3  UNL     1      -2.319   2.607   0.263  1.00  0.00           H  
HETATM   18  H4  UNL     1      -2.159  -2.104   1.471  1.00  0.00           H  
HETATM   19  H5  UNL     1      -3.857  -2.053   0.159  1.00  0.00           H  
HETATM   20  H6  UNL     1      -1.002  -2.217  -1.037  1.00  0.00           H  
HETATM   21  H7  UNL     1      -0.008  -2.031   0.453  1.00  0.00           H  
HETATM   22  H8  UNL     1      -0.520  -0.039  -1.691  1.00  0.00           H  
HETATM   23  H9  UNL     1       1.668  -0.120  -2.267  1.00  0.00           H  
HETATM   24  H10 UNL     1       4.098   0.194  -1.765  1.00  0.00           H  
HETATM   25  H11 UNL     1       4.760   0.513   0.571  1.00  0.00           H  
HETATM   26  H12 UNL     1       0.731   0.213   1.833  1.00  0.00           H  
CONECT    1    2   15   16   17
CONECT    2    3    8
CONECT    3    4    4    5
CONECT    5    6    7   18
CONECT    6   19
CONECT    7    8   20   21
CONECT    8    9   22
CONECT    9   10   10   14
CONECT   10   11   23
CONECT   11   12   12   24
CONECT   12   13   25
CONECT   13   14   14
CONECT   14   26
END

View in JSmol View Stereo Labels

Synonyms

Value	Source
1-Methyl-3-hydroxy-5-(3-pyridyl)-2-pyrrolidinone	MeSH
3'-Hydroxycotinine	MeSH
3-Hydroxycotinine	MeSH

Chemical Formula

C₁₀H₁₂N₂O₂

Average Molecular Weight

192.218

Monoisotopic Molecular Weight

192.089877634

IUPAC Name

3-hydroxy-1-methyl-5-(pyridin-3-yl)pyrrolidin-2-one

Traditional Name

3-hydroxy-1-methyl-5-(pyridin-3-yl)pyrrolidin-2-one

CAS Registry Number

Not Available

SMILES

CN1C(CC(O)C1=O)C1=CC=CN=C1

InChI Identifier

InChI=1S/C10H12N2O2/c1-12-8(5-9(13)10(12)14)7-3-2-4-11-6-7/h2-4,6,8-9,13H,5H2,1H3

InChI Key

XOKCJXZZNAUIQN-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrrolidinylpyridines. Pyrrolidinylpyridines are compounds containing a pyrrolidinylpyridine ring system, which consists of a pyrrolidine ring linked to a pyridine ring.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Pyridines and derivatives

Sub Class

Pyrrolidinylpyridines

Direct Parent

Pyrrolidinylpyridines

Alternative Parents

Substituents

Pyrrolidinylpyridine
Alkaloid or derivatives
Pyrrolidone
2-pyrrolidone
N-alkylpyrrolidine
Pyrrolidine
Tertiary carboxylic acid amide
Heteroaromatic compound
Carboxamide group
Lactam
Secondary alcohol
Carboxylic acid derivative
Azacycle
Organic oxide
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Organooxygen compound
Organonitrogen compound
Alcohol
Carbonyl group
Hydrocarbon derivative
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

a secondary metabolite (CPD-2750 )

Ontology

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	-0.32	ALOGPS
logP	-0.73	ChemAxon
logS	-0.61	ALOGPS
pKa (Strongest Acidic)	13.11	ChemAxon
pKa (Strongest Basic)	4.79	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	53.43 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	50.73 m³·mol⁻¹	ChemAxon
Polarizability	19.51 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	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
AllCCS	[M+H]+	143.02	32859911
AllCCS	[M+H-H2O]+	138.609	32859911
AllCCS	[M+Na]+	148.316	32859911
AllCCS	[M+NH4]+	147.13	32859911
AllCCS	[M-H]-	143.554	32859911
AllCCS	[M+Na-2H]-	143.89	32859911
AllCCS	[M+HCOO]-	144.351	32859911
DeepCCS	[M+H]+	139.597	30932474
DeepCCS	[M-H]-	137.202	30932474
DeepCCS	[M-2H]-	172.511	30932474
DeepCCS	[M+Na]+	147.068	30932474

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Predicted by Siyang on May 30, 2022	8.4514 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	2.43 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	530.5 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	243.9 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	78.3 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	156.0 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	38.9 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	229.2 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	251.8 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	246.4 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	563.0 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	41.7 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	716.8 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	174.0 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	179.0 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	482.3 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	425.2 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	192.7 seconds	40023050

Predicted Kovats Retention Indices

Not Available

Spectra

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - trans-3'-hydroxycotinine 10V, Positive-QTOF	splash10-0006-0900000000-10491466da607f26af40	2015-05-27	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - trans-3'-hydroxycotinine 20V, Positive-QTOF	splash10-002f-0900000000-78f82d7b225d0b0b2997	2015-05-27	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - trans-3'-hydroxycotinine 40V, Positive-QTOF	splash10-0aou-7900000000-0dd265836ac28cc4dc52	2015-05-27	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - trans-3'-hydroxycotinine 10V, Negative-QTOF	splash10-0006-0900000000-507db3f71e793a37d79a	2015-05-27	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - trans-3'-hydroxycotinine 20V, Negative-QTOF	splash10-0006-1900000000-dc50aba7536d41b87f1b	2015-05-27	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - trans-3'-hydroxycotinine 40V, Negative-QTOF	splash10-004i-9800000000-3acee66b7383c0812ac9	2015-05-27	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - trans-3'-hydroxycotinine 10V, Positive-QTOF	splash10-000f-0900000000-ef6a1b4845a8cb3fafe9	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - trans-3'-hydroxycotinine 20V, Positive-QTOF	splash10-009g-0900000000-c79c308d9471325ffcbf	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - trans-3'-hydroxycotinine 40V, Positive-QTOF	splash10-0536-6900000000-82585081ee4cac8d3df6	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - trans-3'-hydroxycotinine 10V, Negative-QTOF	splash10-0006-0900000000-e7b2f7bcd35785f3b3bd	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - trans-3'-hydroxycotinine 20V, Negative-QTOF	splash10-002f-5900000000-020796e72efc2843cc0c	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - trans-3'-hydroxycotinine 40V, Negative-QTOF	splash10-004i-9400000000-d125ee5fd9a8ba289261	2021-10-21	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood
Urine

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Cancer patients undergoing total body irradiation	31424920	details
Urine	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Cancer patients undergoing total body irradiation	31424920	details

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

FDB031206

KNApSAcK ID

Not Available

Chemspider ID

401

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

414

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

Not Available

Showing metabocard for trans-3'-hydroxycotinine (HMDB0304504)

MOL for HMDB0304504 (trans-3'-hydroxycotinine)

3D MOL for HMDB0304504 (trans-3'-hydroxycotinine)

3D SDF for HMDB0304504 (trans-3'-hydroxycotinine)

3D-SDF for HMDB0304504 (trans-3'-hydroxycotinine)

PDB for HMDB0304504 (trans-3'-hydroxycotinine)

3D PDB for HMDB0304504 (trans-3'-hydroxycotinine)

SMILES for HMDB0304504 (trans-3'-hydroxycotinine)

INCHI for HMDB0304504 (trans-3'-hydroxycotinine)

Structure for HMDB0304504 (trans-3'-hydroxycotinine)

3D Structure for HMDB0304504 (trans-3'-hydroxycotinine)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

MS/MS Spectra