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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2013-07-09 16:12:46 UTC

Update Date

2023-02-21 17:30:18 UTC

HMDB ID

HMDB0061017

Secondary Accession Numbers

HMDB61017

Metabolite Identification

Common Name

1-Pyrimidinylpiperazine

Description

1-Pyrimidinylpiperazine is a metabolite of buspirone. Buspirone is an anxiolytic psychoactive drug of the azapirone chemical class, and is primarily used to treat generalized anxiety disorder (GAD) Bristol-Myers Squibb (BMS) gained FDA approval of buspirone in 1986 for treatment of GAD. The patent on Buspar by Bristol-Myers Squibb expired in 2001, and buspirone is available as a generic. (Wikipedia )

Structure

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

HEADER    PROTEIN                                 27-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 490                                               
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-FEB-12         0                                  
HETATM    1  N   UNK     0      10.780   2.001   0.000  0.00  0.00           N+0
HETATM    2  N   UNK     0       7.700   2.001   0.000  0.00  0.00           N+0
HETATM    3  N   UNK     0       5.390   0.667   0.000  0.00  0.00           N+0
HETATM    4  N   UNK     0       5.390   3.334   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0      10.010   0.667   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      10.010   3.334   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       8.470   0.667   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       8.470   3.334   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.160   2.001   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.850   0.667   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.850   3.334   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.080   2.001   0.000  0.00  0.00           C+0
CONECT    1    5    6                                                       
CONECT    2    7    8    9                                                  
CONECT    3    9   10                                                       
CONECT    4    9   11                                                       
CONECT    5    1    7                                                       
CONECT    6    1    8                                                       
CONECT    7    2    5                                                       
CONECT    8    2    6                                                       
CONECT    9    2    3    4                                                  
CONECT   10    3   12                                                       
CONECT   11    4   12                                                       
CONECT   12   10   11                                                       
MASTER        0    0    0    0    0    0    0    0   12    0   26    0
END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
1-(2-Pyrimidinyl)piperazine	HMDB

Chemical Formula

C₈H₁₂N₄

Average Molecular Weight

164.2077

Monoisotopic Molecular Weight

164.106196404

IUPAC Name

2-(piperazin-1-yl)pyrimidine

Traditional Name

pyrimidinylpiperazine

CAS Registry Number

Not Available

SMILES

C1CN(CCN1)C1=NC=CC=N1

InChI Identifier

InChI=1S/C8H12N4/c1-2-10-8(11-3-1)12-6-4-9-5-7-12/h1-3,9H,4-7H2

InChI Key

MRBFGEHILMYPTF-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as n-arylpiperazines. These are organic compounds containing a piperazine ring where the nitrogen ring atom carries an aryl group.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Diazinanes

Sub Class

Piperazines

Direct Parent

N-arylpiperazines

Alternative Parents

Substituents

N-arylpiperazine
Dialkylarylamine
Aminopyrimidine
Pyrimidine
Heteroaromatic compound
Azacycle
Secondary amine
Secondary aliphatic amine
Organic nitrogen compound
Organopnictogen compound
Hydrocarbon derivative
Organonitrogen compound
Amine
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Cytoplasm (HMDB: HMDB0061017)

Non-excretory biofluid

Biofluid or Excreta

Blood (HMDB: HMDB0061017)

Organ

Kidney (HMDB: HMDB0061017)
Liver (HMDB: HMDB0061017)

Excreta

Biofluid or Excreta

Urine (HMDB: HMDB0061017)

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
Water Solubility	5.02 g/L	ALOGPS
logP	0.32	ALOGPS
logP	0.3	ChemAxon
logS	-1.5	ALOGPS
pKa (Strongest Basic)	8.69	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	41.05 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	47.85 m³·mol⁻¹	ChemAxon
Polarizability	17.65 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
DarkChem	[M+H]+	135.461	31661259
DarkChem	[M-H]-	131.503	31661259
DeepCCS	[M+H]+	130.64	30932474
DeepCCS	[M-H]-	126.807	30932474
DeepCCS	[M-2H]-	163.938	30932474
DeepCCS	[M+Na]+	139.478	30932474
AllCCS	[M+H]+	136.5	32859911
AllCCS	[M+H-H2O]+	132.0	32859911
AllCCS	[M+NH4]+	140.7	32859911
AllCCS	[M+Na]+	142.0	32859911
AllCCS	[M-H]-	137.2	32859911
AllCCS	[M+Na-2H]-	138.0	32859911
AllCCS	[M+HCOO]-	139.0	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
1-Pyrimidinylpiperazine	C1CN(CCN1)C1=NC=CC=N1	2219.6	Standard polar	33892256
1-Pyrimidinylpiperazine	C1CN(CCN1)C1=NC=CC=N1	1485.6	Standard non polar	33892256
1-Pyrimidinylpiperazine	C1CN(CCN1)C1=NC=CC=N1	1528.2	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
1-Pyrimidinylpiperazine,1TMS,isomer #1	C[Si](C)(C)N1CCN(C2=NC=CC=N2)CC1	1806.0	Semi standard non polar	33892256
1-Pyrimidinylpiperazine,1TMS,isomer #1	C[Si](C)(C)N1CCN(C2=NC=CC=N2)CC1	1738.0	Standard non polar	33892256
1-Pyrimidinylpiperazine,1TMS,isomer #1	C[Si](C)(C)N1CCN(C2=NC=CC=N2)CC1	2464.7	Standard polar	33892256
1-Pyrimidinylpiperazine,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1CCN(C2=NC=CC=N2)CC1	2022.8	Semi standard non polar	33892256
1-Pyrimidinylpiperazine,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1CCN(C2=NC=CC=N2)CC1	1983.3	Standard non polar	33892256
1-Pyrimidinylpiperazine,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1CCN(C2=NC=CC=N2)CC1	2679.9	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 1-Pyrimidinylpiperazine GC-MS (Non-derivatized) - 70eV, Positive	splash10-06yx-7900000000-7890a03165f2578c27b2	2017-09-20	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 1-Pyrimidinylpiperazine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 1-Pyrimidinylpiperazine 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-Pyrimidinylpiperazine 10V, Positive-QTOF	splash10-014i-0900000000-5d73c4e22666b2854fa2	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Pyrimidinylpiperazine 20V, Positive-QTOF	splash10-014i-0900000000-146a9c9a05074217089f	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Pyrimidinylpiperazine 40V, Positive-QTOF	splash10-006y-9400000000-cac7fcf23570f1dacb4b	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Pyrimidinylpiperazine 10V, Negative-QTOF	splash10-03di-0900000000-a145049f166ff28cd8ca	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Pyrimidinylpiperazine 20V, Negative-QTOF	splash10-03di-0900000000-802f9e24a28787a8d736	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Pyrimidinylpiperazine 40V, Negative-QTOF	splash10-0f6x-9200000000-14f6f18a0017b6c8f5cb	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Pyrimidinylpiperazine 10V, Positive-QTOF	splash10-014i-0900000000-73928c0aa7d69003250a	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Pyrimidinylpiperazine 20V, Positive-QTOF	splash10-014i-0900000000-a2dca1cc0f984170add2	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Pyrimidinylpiperazine 40V, Positive-QTOF	splash10-006t-9500000000-324e0e5e6e2e39824388	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Pyrimidinylpiperazine 10V, Negative-QTOF	splash10-03di-0900000000-19daf282229d1771895d	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Pyrimidinylpiperazine 20V, Negative-QTOF	splash10-03di-4900000000-fdf03b9d17e6a26c01ea	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Pyrimidinylpiperazine 40V, Negative-QTOF	splash10-014i-9200000000-cf31c66127a5e9f752ee	2021-09-24	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-24	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

Cytoplasm

Biospecimen Locations

Blood
Urine

Tissue Locations

Kidney
Liver

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Not Available	Not Available	Normal	Not Available	details
Urine	Expected but not Quantified	Not Quantified	Not Available	Not Available	Normal	Not Available	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

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Pyrimidinylpiperazine

METLIN ID

Not Available

PubChem Compound

88747

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 1-Pyrimidinylpiperazine (HMDB0061017)

MOL for HMDB0061017 (1-Pyrimidinylpiperazine)

3D MOL for HMDB0061017 (1-Pyrimidinylpiperazine)

3D SDF for HMDB0061017 (1-Pyrimidinylpiperazine)

3D-SDF for HMDB0061017 (1-Pyrimidinylpiperazine)

PDB for HMDB0061017 (1-Pyrimidinylpiperazine)

3D PDB for HMDB0061017 (1-Pyrimidinylpiperazine)

SMILES for HMDB0061017 (1-Pyrimidinylpiperazine)

INCHI for HMDB0061017 (1-Pyrimidinylpiperazine)

Structure for HMDB0061017 (1-Pyrimidinylpiperazine)

3D Structure for HMDB0061017 (1-Pyrimidinylpiperazine)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra