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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2017-03-16 03:38:55 UTC

Update Date

2023-02-21 17:30:46 UTC

HMDB ID

HMDB0062266

Secondary Accession Numbers

HMDB62266

Metabolite Identification

Common Name

1-(3-Pyridinyl)-1,4-butanediol

Description

1-(pyridin-3-yl)butane-1,4-diol belongs to the class of organic compounds known as pyridines and derivatives. Pyridines and derivatives are compounds containing a pyridine ring, which is a six-member aromatic heterocycle which consists of one nitrogen atom and five carbon atoms. 1-(pyridin-3-yl)butane-1,4-diol is a strong basic compound (based on its pKa).

Structure

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

HEADER    PROTEIN                                 16-MAR-17   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   16-MAR-17         0                                  
HETATM    1  O   UNK     0       0.000  -4.620   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       5.335  -3.080   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       6.668  -5.390   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       9.336  -5.390   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       9.336  -6.930   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       8.002  -7.700   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.668  -6.930   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8   12                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11    7                                                       
MASTER        0    0    0    0    0    0    0    0   12    0   24    0
END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₉H₁₃NO₂

Average Molecular Weight

167.208

Monoisotopic Molecular Weight

167.094628663

IUPAC Name

1-(pyridin-3-yl)butane-1,4-diol

Traditional Name

1-(pyridin-3-yl)butane-1,4-diol

CAS Registry Number

76014-83-0

SMILES

OCCCC(O)C1=CN=CC=C1

InChI Identifier

InChI=1S/C9H13NO2/c11-6-2-4-9(12)8-3-1-5-10-7-8/h1,3,5,7,9,11-12H,2,4,6H2

InChI Key

RGJHRVMTLGLFPX-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyridines and derivatives. Pyridines and derivatives are compounds containing a pyridine ring, which is a six-member aromatic heterocycle which consists of one nitrogen atom and five carbon atoms.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Pyridines and derivatives

Sub Class

Not Available

Direct Parent

Pyridines and derivatives

Alternative Parents

Substituents

Pyridine
Heteroaromatic compound
Secondary alcohol
Azacycle
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Hydrocarbon derivative
Aromatic alcohol
Primary alcohol
Organooxygen compound
Organonitrogen compound
Alcohol
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

pyridines (CHEBI:82576 )

Ontology

Not Available

Not Available

Not Available

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	49.7 g/l	ALOGPS
LogP	0.02	ALOGPS

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	0.02	ALOGPS
logP	-0.065	ChemAxon
logS	-0.53	ALOGPS
pKa (Strongest Acidic)	14.22	ChemAxon
pKa (Strongest Basic)	4.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	53.35 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	46.19 m³·mol⁻¹	ChemAxon
Polarizability	18.15 Å³	ChemAxon
Number of Rings	1	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
DarkChem	[M+H]+	136.075	31661259
DarkChem	[M-H]-	132.589	31661259
DeepCCS	[M+H]+	137.98	30932474
DeepCCS	[M-H]-	134.15	30932474
DeepCCS	[M-2H]-	171.697	30932474
DeepCCS	[M+Na]+	147.176	30932474
AllCCS	[M+H]+	137.3	32859911
AllCCS	[M+H-H2O]+	133.0	32859911
AllCCS	[M+NH4]+	141.4	32859911
AllCCS	[M+Na]+	142.6	32859911
AllCCS	[M-H]-	137.9	32859911
AllCCS	[M+Na-2H]-	139.0	32859911
AllCCS	[M+HCOO]-	140.3	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
1-(3-Pyridinyl)-1,4-butanediol	OCCCC(O)C1=CN=CC=C1	2456.4	Standard polar	33892256
1-(3-Pyridinyl)-1,4-butanediol	OCCCC(O)C1=CN=CC=C1	1574.8	Standard non polar	33892256
1-(3-Pyridinyl)-1,4-butanediol	OCCCC(O)C1=CN=CC=C1	1647.1	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
1-(3-Pyridinyl)-1,4-butanediol,1TMS,isomer #1	C[Si](C)(C)OCCCC(O)C1=CC=CN=C1	1658.4	Semi standard non polar	33892256
1-(3-Pyridinyl)-1,4-butanediol,1TMS,isomer #2	C[Si](C)(C)OC(CCCO)C1=CC=CN=C1	1625.8	Semi standard non polar	33892256
1-(3-Pyridinyl)-1,4-butanediol,2TMS,isomer #1	C[Si](C)(C)OCCCC(O[Si](C)(C)C)C1=CC=CN=C1	1654.3	Semi standard non polar	33892256
1-(3-Pyridinyl)-1,4-butanediol,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCCCC(O)C1=CC=CN=C1	1876.5	Semi standard non polar	33892256
1-(3-Pyridinyl)-1,4-butanediol,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC(CCCO)C1=CC=CN=C1	1834.2	Semi standard non polar	33892256
1-(3-Pyridinyl)-1,4-butanediol,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCCCC(O[Si](C)(C)C(C)(C)C)C1=CC=CN=C1	2094.5	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 - 1-(3-Pyridinyl)-1,4-butanediol GC-MS (Non-derivatized) - 70eV, Positive	splash10-0a4i-5900000000-5824b68784483fc8cf24	2017-09-20	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 1-(3-Pyridinyl)-1,4-butanediol GC-MS (2 TMS) - 70eV, Positive	splash10-001i-5920000000-bcf7d67f28fa716802ab	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 1-(3-Pyridinyl)-1,4-butanediol GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 1-(3-Pyridinyl)-1,4-butanediol 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 - 1-(3-Pyridinyl)-1,4-butanediol 10V, Positive-QTOF	splash10-0uxr-0900000000-671cf200babb7ca038d8	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-(3-Pyridinyl)-1,4-butanediol 20V, Positive-QTOF	splash10-0ue9-2900000000-5800615362103331e7b3	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-(3-Pyridinyl)-1,4-butanediol 40V, Positive-QTOF	splash10-0536-9600000000-a5aa47182b334e113963	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-(3-Pyridinyl)-1,4-butanediol 10V, Negative-QTOF	splash10-014i-0900000000-6ffb27174de06f038aae	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-(3-Pyridinyl)-1,4-butanediol 20V, Negative-QTOF	splash10-014j-2900000000-bb8e6eefe8522a6733ff	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-(3-Pyridinyl)-1,4-butanediol 40V, Negative-QTOF	splash10-004i-9200000000-89493b08484d5f5421e6	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-(3-Pyridinyl)-1,4-butanediol 10V, Positive-QTOF	splash10-0gb9-0900000000-653ec9dcc0ac04d37cc8	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-(3-Pyridinyl)-1,4-butanediol 20V, Positive-QTOF	splash10-00di-3900000000-8cbe8499202d3f62fdda	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-(3-Pyridinyl)-1,4-butanediol 40V, Positive-QTOF	splash10-053r-9500000000-8c0003adf497fe9349c0	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-(3-Pyridinyl)-1,4-butanediol 10V, Negative-QTOF	splash10-014i-1900000000-e82416a6acaef850938e	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-(3-Pyridinyl)-1,4-butanediol 20V, Negative-QTOF	splash10-004i-9800000000-dab153894e9bea7e166d	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-(3-Pyridinyl)-1,4-butanediol 40V, Negative-QTOF	splash10-004i-9400000000-9eb5d1033d15969281d6	2021-09-22	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum

IR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)	2023-02-04	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)	2023-02-04	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)	2023-02-04	FELIX lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

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

Not Available

KEGG Compound ID

C19582

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

156653

PDB ID

Not Available

ChEBI ID

82576

Food Biomarker Ontology

Not Available

VMH ID

M00225

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 1-(3-Pyridinyl)-1,4-butanediol (HMDB0062266)

MOL for HMDB0062266 (1-(3-Pyridinyl)-1,4-butanediol)

3D MOL for HMDB0062266 (1-(3-Pyridinyl)-1,4-butanediol)

3D SDF for HMDB0062266 (1-(3-Pyridinyl)-1,4-butanediol)

3D-SDF for HMDB0062266 (1-(3-Pyridinyl)-1,4-butanediol)

PDB for HMDB0062266 (1-(3-Pyridinyl)-1,4-butanediol)

3D PDB for HMDB0062266 (1-(3-Pyridinyl)-1,4-butanediol)

SMILES for HMDB0062266 (1-(3-Pyridinyl)-1,4-butanediol)

INCHI for HMDB0062266 (1-(3-Pyridinyl)-1,4-butanediol)

Structure for HMDB0062266 (1-(3-Pyridinyl)-1,4-butanediol)

3D Structure for HMDB0062266 (1-(3-Pyridinyl)-1,4-butanediol)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra