MiMeDB: Showing metabocard for (R)-piperazine-2-carboxylic acid (MMDBc0055049)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-17 19:40:46 UTC

Update Date

2025-10-07 16:08:53 UTC

Metabolite ID

MMDBc0055049

Metabolite Identification

Common Name

(R)-piperazine-2-carboxylic acid

Description

(R)-piperazine-2-carboxylic acid is a member of the piperazine chemical class, characterized by a piperazine ring with a carboxylic acid functional group at the 2-position. This compound plays a role in various biochemical pathways, particularly as a metabolite in the degradation of piperazine derivatives. The enzyme R-amidase has been shown to act R-stereoselectively on (R,S)-piperazine-2-tert-butylcarboxamide, converting it into (R)-piperazine-2-carboxylic acid (PMID:15066183 ). This stereoselective transformation highlights the compound's relevance in enzymatic reactions and metabolic processes involving piperazine compounds. The presence of the carboxylic acid group not only contributes to its solubility and reactivity but also suggests potential interactions with biological systems, including its involvement in amino acid metabolism and neurotransmitter pathways. Understanding the chemical structure and pathways associated with (R)-piperazine-2-carboxylic acid can provide insights into its functional roles in various biological contexts.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
(R)-2-Piperazinecarboxylate	Kegg
(R)-2-Piperazinecarboxylic acid	Generator
(R)-Piperazine-2-carboxylate	Generator

Molecular Formula

C₅H₁₀N₂O₂

Average Mass

130.147

Monoisotopic Mass

130.07422757

IUPAC Name

(2R)-piperazine-2-carboxylic acid

Traditional Name

(2R)-piperazine-2-carboxylic acid

CAS Registry Number

Not Available

SMILES

[H][C@@]1(CNCCN1)C(O)=O

InChI Identifier

InChI=1S/C5H10N2O2/c8-5(9)4-3-6-1-2-7-4/h4,6-7H,1-3H2,(H,8,9)/t4-/m1/s1

InChI Key

JSSXHAMIXJGYCS-SCSAIBSYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as d-alpha-amino acids. These are alpha amino acids which have the D-configuration of the alpha-carbon atom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

D-alpha-amino acids

Alternative Parents

Substituents

D-alpha-amino acid
Piperazine-2-carboxylic acid
1,4-diazinane
Piperazine
Amino acid
Carboxylic acid
Secondary aliphatic amine
Monocarboxylic acid or derivatives
Secondary amine
Organoheterocyclic compound
Azacycle
Organic nitrogen compound
Organooxygen compound
Organonitrogen compound
Carbonyl group
Amine
Organopnictogen compound
Organic oxide
Organic oxygen compound
Hydrocarbon derivative
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

piperazinecarboxylic acid (CHEBI:55357 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-3.5	ChemAxon
pKa (Strongest Acidic)	1.31	ChemAxon
pKa (Strongest Basic)	9.48	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	61.36 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	31.28 m³·mol⁻¹	ChemAxon
Polarizability	12.84 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	Not Available	2022-08-10	View Spectrum
MS	Mass Spectrum (Electron Ionization)	Not Available	2022-08-06	View Spectrum

Chromatographic Retention Times and Retention Indices

Retention Times

Chromatography Type	Technique	Column	Deposition Date	Retention Time (s)
Liquid Chromatography	HILIC	Waters Acquity UPLC-BEH Amide column (eluted)	2025-10-24	512.0
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-24	421.3
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (void)	2025-10-24	40.7
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-24	218.5
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-24	306.5
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (void)	2025-10-24	326.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-24	419.2
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	942.4
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-24	805.1
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-24	194.6
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	546.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-24	209.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-24	36.4
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	360.7
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	758.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-24	95.8
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-24	331.9
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-24	657.7
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-24	593.9

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	(R)-piperazine-2-carboxylic acid_TMS_1	C[Si](C)(C)OC(=O)[C@H]1CNCCN1	standard non polar	2025-10-24	1697.41
Gas Chromatography	(R)-piperazine-2-carboxylic acid_TMS_2	C[Si](C)(C)N1CCN[C@@H](C(=O)O)C1	standard non polar	2025-10-24	1731.06
Gas Chromatography	(R)-piperazine-2-carboxylic acid_TMS_3	C[Si](C)(C)N1CCNC[C@@H]1C(=O)O	standard non polar	2025-10-24	2082.99
Gas Chromatography	(R)-piperazine-2-carboxylic acid_TMS_4	C[Si](C)(C)OC(=O)[C@H]1CN([Si](C)(C)C)CCN1	standard non polar	2025-10-24	1772.46
Gas Chromatography	(R)-piperazine-2-carboxylic acid_TMS_5	C[Si](C)(C)OC(=O)[C@H]1CNCCN1[Si](C)(C)C	standard non polar	2025-10-24	1796.89
Gas Chromatography	(R)-piperazine-2-carboxylic acid_TMS_6	C[Si](C)(C)N1CCN([Si](C)(C)C)[C@@H](C(=O)O)C1	standard non polar	2025-10-24	2430.2
Gas Chromatography	(R)-piperazine-2-carboxylic acid_TMS_7	C[Si](C)(C)OC(=O)[C@H]1CN([Si](C)(C)C)CCN1[Si](C)(C)C	standard non polar	2025-10-24	2110.7
Gas Chromatography	(R)-piperazine-2-carboxylic acid_TMS_1	C[Si](C)(C)OC(=O)[C@H]1CNCCN1	standard polar	2025-10-24	2437.35
Gas Chromatography	(R)-piperazine-2-carboxylic acid_TMS_2	C[Si](C)(C)N1CCN[C@@H](C(=O)O)C1	standard polar	2025-10-24	2026.47
Gas Chromatography	(R)-piperazine-2-carboxylic acid_TMS_3	C[Si](C)(C)N1CCNC[C@@H]1C(=O)O	standard polar	2025-10-24	1899.3
Gas Chromatography	(R)-piperazine-2-carboxylic acid_TMS_4	C[Si](C)(C)OC(=O)[C@H]1CN([Si](C)(C)C)CCN1	standard polar	2025-10-24	2211.32
Gas Chromatography	(R)-piperazine-2-carboxylic acid_TMS_5	C[Si](C)(C)OC(=O)[C@H]1CNCCN1[Si](C)(C)C	standard polar	2025-10-24	1764.51
Gas Chromatography	(R)-piperazine-2-carboxylic acid_TMS_6	C[Si](C)(C)N1CCN([Si](C)(C)C)[C@@H](C(=O)O)C1	standard polar	2025-10-24	2345.58
Gas Chromatography	(R)-piperazine-2-carboxylic acid_TMS_7	C[Si](C)(C)OC(=O)[C@H]1CN([Si](C)(C)C)CCN1[Si](C)(C)C	standard polar	2025-10-24	2350.89

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria	Proteobacteria	1	Human feces; Human

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

5027799

KEGG Compound ID

C19780

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

6558437

PDB ID

Not Available

ChEBI ID

55357

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for (R)-piperazine-2-carboxylic acid (MMDBc0055049)

MOL for #<Metabolite:0x00007f9a9a5d8428>

3D MOL for #<Metabolite:0x00007f9a9a5d8428>

3D SDF for #<Metabolite:0x00007f9a9a5d8428>

3D-SDF for #<Metabolite:0x00007f9a9a5d8428>

PDB for #<Metabolite:0x00007f9a9a5d8428>

3D PDB for #<Metabolite:0x00007f9a9a5d8428>

SMILES for #<Metabolite:0x00007f9a9a5d8428>

INCHI for #<Metabolite:0x00007f9a9a5d8428>

Structure for #<Metabolite:0x00007f9a9a5d8428>

3D Structure for #<Metabolite:0x00007f9a9a5d8428>