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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 20:58:04 UTC

Update Date

2022-11-23 22:29:20 UTC

HMDB ID

HMDB0259050

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Thurfyl Nicotinate

Description

Thurfyl Nicotinate, also known as trafuril, belongs to the class of organic compounds known as pyridinecarboxylic acids. Pyridinecarboxylic acids are compounds containing a pyridine ring bearing a carboxylic acid group. Based on a literature review very few articles have been published on Thurfyl Nicotinate. This compound has been identified in human blood as reported by (PMID: 31557052 ). Thurfyl nicotinate is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Thurfyl Nicotinate 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


  Mrv1652309112122582D          

 15 16  0  0  0  0            999 V2000
    2.3387   -3.8062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0837   -3.0215    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512   -2.5366    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4186   -3.0215    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1637   -3.8062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512   -1.7116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4656   -1.2991    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4656   -0.4741    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512   -0.0616    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1801   -0.0616    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1801    0.7634    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8946    1.1759    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.6091    0.7634    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6091   -0.0616    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8946   -0.4741    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
  1  5  1  0  0  0  0
  3  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 10 15  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0259050

> <DATABASE_NAME>
hmdb

> <SMILES>
O=C(OCC1CCCO1)C1=CN=CC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C11H13NO3/c13-11(9-3-1-5-12-7-9)15-8-10-4-2-6-14-10/h1,3,5,7,10H,2,4,6,8H2

> <INCHI_KEY>
RQAITHJHUFFEIV-UHFFFAOYSA-N

> <FORMULA>
C11H13NO3

> <MOLECULAR_WEIGHT>
207.229

> <EXACT_MASS>
207.089543283

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
28

> <JCHEM_AVERAGE_POLARIZABILITY>
21.620677593820666

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(oxolan-2-yl)methyl pyridine-3-carboxylate

> <ALOGPS_LOGP>
1.15

> <JCHEM_LOGP>
1.1776393813333335

> <ALOGPS_LOGS>
-0.82

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
3.242041993441245

> <JCHEM_POLAR_SURFACE_AREA>
48.42

> <JCHEM_REFRACTIVITY>
54.181100000000015

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.12e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
thurfyl nicotinate

> <JCHEM_VEBER_RULE>
0

$$$$

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       4.366  -7.105   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.890  -5.640   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.136  -4.735   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       6.381  -5.640   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       5.906  -7.105   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.136  -3.195   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       6.469  -2.425   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       6.469  -0.885   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       5.136  -0.115   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       7.803  -0.115   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       7.803   1.425   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0       9.137   2.195   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0      10.470   1.425   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      10.470  -0.115   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       9.137  -0.885   0.000  0.00  0.00           C+0
CONECT    1    2    5                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4    6                                                  
CONECT    4    3    5                                                       
CONECT    5    4    1                                                       
CONECT    6    3    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   15                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   10                                                       
MASTER        0    0    0    0    0    0    0    0   15    0   32    0
END

COMPND    HMDB0259050
HETATM    1  O1  UNL     1       0.434   0.694   1.740  1.00  0.00           O  
HETATM    2  C1  UNL     1       1.053  -0.062   0.950  1.00  0.00           C  
HETATM    3  O2  UNL     1       0.338  -1.045   0.316  1.00  0.00           O  
HETATM    4  C2  UNL     1      -1.040  -1.256   0.496  1.00  0.00           C  
HETATM    5  C3  UNL     1      -1.885  -0.078   0.121  1.00  0.00           C  
HETATM    6  C4  UNL     1      -3.342  -0.558   0.120  1.00  0.00           C  
HETATM    7  C5  UNL     1      -3.999   0.520  -0.701  1.00  0.00           C  
HETATM    8  C6  UNL     1      -2.827   1.132  -1.450  1.00  0.00           C  
HETATM    9  O3  UNL     1      -1.736   0.285  -1.215  1.00  0.00           O  
HETATM   10  C7  UNL     1       2.473   0.067   0.690  1.00  0.00           C  
HETATM   11  C8  UNL     1       3.115  -0.773  -0.175  1.00  0.00           C  
HETATM   12  C9  UNL     1       4.458  -0.634  -0.406  1.00  0.00           C  
HETATM   13  C10 UNL     1       5.129   0.366   0.253  1.00  0.00           C  
HETATM   14  N1  UNL     1       4.526   1.210   1.112  1.00  0.00           N  
HETATM   15  C11 UNL     1       3.205   1.063   1.332  1.00  0.00           C  
HETATM   16  H1  UNL     1      -1.291  -1.530   1.541  1.00  0.00           H  
HETATM   17  H2  UNL     1      -1.330  -2.106  -0.160  1.00  0.00           H  
HETATM   18  H3  UNL     1      -1.807   0.780   0.788  1.00  0.00           H  
HETATM   19  H4  UNL     1      -3.728  -0.627   1.136  1.00  0.00           H  
HETATM   20  H5  UNL     1      -3.355  -1.510  -0.448  1.00  0.00           H  
HETATM   21  H6  UNL     1      -4.463   1.247   0.006  1.00  0.00           H  
HETATM   22  H7  UNL     1      -4.764   0.122  -1.395  1.00  0.00           H  
HETATM   23  H8  UNL     1      -2.544   2.124  -1.011  1.00  0.00           H  
HETATM   24  H9  UNL     1      -3.033   1.211  -2.538  1.00  0.00           H  
HETATM   25  H10 UNL     1       2.576  -1.559  -0.691  1.00  0.00           H  
HETATM   26  H11 UNL     1       4.994  -1.282  -1.085  1.00  0.00           H  
HETATM   27  H12 UNL     1       6.177   0.496   0.091  1.00  0.00           H  
HETATM   28  H13 UNL     1       2.665   1.701   2.003  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   10
CONECT    3    4
CONECT    4    5   16   17
CONECT    5    6    9   18
CONECT    6    7   19   20
CONECT    7    8   21   22
CONECT    8    9   23   24
CONECT   10   11   11   15
CONECT   11   12   25
CONECT   12   13   13   26
CONECT   13   14   27
CONECT   14   15   15
CONECT   15   28
END

View in JSmol View Stereo Labels

Synonyms

Value	Source
Thurfyl nicotinic acid	Generator
(Oxolan-2-yl)methyl pyridine-3-carboxylic acid	HMDB
Trafuril	HMDB
Tetrahydrofurfuryl nicotinate	HMDB

Chemical Formula

C₁₁H₁₃NO₃

Average Molecular Weight

207.229

Monoisotopic Molecular Weight

207.089543283

IUPAC Name

(oxolan-2-yl)methyl pyridine-3-carboxylate

Traditional Name

thurfyl nicotinate

CAS Registry Number

Not Available

SMILES

O=C(OCC1CCCO1)C1=CN=CC=C1

InChI Identifier

InChI=1S/C11H13NO3/c13-11(9-3-1-5-12-7-9)15-8-10-4-2-6-14-10/h1,3,5,7,10H,2,4,6,8H2

InChI Key

RQAITHJHUFFEIV-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyridinecarboxylic acids. Pyridinecarboxylic acids are compounds containing a pyridine ring bearing a carboxylic acid group.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Pyridines and derivatives

Sub Class

Pyridinecarboxylic acids and derivatives

Direct Parent

Pyridinecarboxylic acids

Alternative Parents

Substituents

Pyridine carboxylic acid
Tetrahydrofuran
Heteroaromatic compound
Carboxylic acid ester
Carboxylic acid derivative
Dialkyl ether
Ether
Monocarboxylic acid or derivatives
Azacycle
Oxacycle
Organooxygen compound
Organonitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic nitrogen compound
Organic oxide
Hydrocarbon derivative
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic 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	1.15	ALOGPS
logP	1.18	ChemAxon
logS	-0.82	ALOGPS
pKa (Strongest Basic)	3.24	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	48.42 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	54.18 m³·mol⁻¹	ChemAxon
Polarizability	21.62 Å³	ChemAxon
Number of Rings	2	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]+	145.737	30932474
DeepCCS	[M-H]-	143.101	30932474
DeepCCS	[M-2H]-	178.975	30932474
DeepCCS	[M+Na]+	154.513	30932474
AllCCS	[M+H]+	147.2	32859911
AllCCS	[M+H-H2O]+	143.0	32859911
AllCCS	[M+NH4]+	151.1	32859911
AllCCS	[M+Na]+	152.2	32859911
AllCCS	[M-H]-	148.7	32859911
AllCCS	[M+Na-2H]-	149.0	32859911
AllCCS	[M+HCOO]-	149.4	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
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.	4.32 minutes	32390414
Predicted by Siyang on May 30, 2022	10.7902 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	2.6 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1965.4 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	276.7 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	134.4 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	168.9 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	97.3 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	384.7 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	474.3 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	79.9 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	795.9 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	87.3 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	1314.5 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	301.7 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	303.0 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	438.1 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	386.6 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	132.6 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
THURFYL NICOTINATE	O=C(OCC1CCCO1)C1=CN=CC=C1	2433.5	Standard polar	33892256
THURFYL NICOTINATE	O=C(OCC1CCCO1)C1=CN=CC=C1	1669.0	Standard non polar	33892256
THURFYL NICOTINATE	O=C(OCC1CCCO1)C1=CN=CC=C1	1709.6	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 - Thurfyl Nicotinate GC-MS (Non-derivatized) - 70eV, Positive	splash10-00bc-9200000000-886516f2fbd407be29c2	2021-09-24	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Thurfyl Nicotinate GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	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

6024

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

6260

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 Thurfyl Nicotinate (HMDB0259050)

MOL for HMDB0259050 (Thurfyl Nicotinate)

3D MOL for HMDB0259050 (Thurfyl Nicotinate)

3D SDF for HMDB0259050 (Thurfyl Nicotinate)

3D-SDF for HMDB0259050 (Thurfyl Nicotinate)

PDB for HMDB0259050 (Thurfyl Nicotinate)

3D PDB for HMDB0259050 (Thurfyl Nicotinate)

SMILES for HMDB0259050 (Thurfyl Nicotinate)

INCHI for HMDB0259050 (Thurfyl Nicotinate)

Structure for HMDB0259050 (Thurfyl Nicotinate)

3D Structure for HMDB0259050 (Thurfyl Nicotinate)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra