Jump To Section:

Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References XML

Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-01 20:05:50 UTC

Update Date

2021-09-26 22:49:00 UTC

HMDB ID

HMDB0242583

Secondary Accession Numbers

None

Metabolite Identification

Common Name

(2R,4S)-Pyrrolidine-2,4-dicarboxylic acid

Description

(2R,4S)-Pyrrolidine-2,4-dicarboxylic acid, also known as 2,4-pyrrolidinedicarboxylate or PDC-2,4, belongs to the class of organic compounds known as proline and derivatives. Proline and derivatives are compounds containing proline or a derivative thereof resulting from reaction of proline at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. Based on a literature review very few articles have been published on (2R,4S)-Pyrrolidine-2,4-dicarboxylic acid. This compound has been identified in human blood as reported by (PMID: 31557052 ). (2r,4s)-pyrrolidine-2,4-dicarboxylic acid is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically (2R,4S)-Pyrrolidine-2,4-dicarboxylic acid 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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
(2R,4S)-Pyrrolidine-2,4-dicarboxylate	Generator
Pyrrolidine-2,4-dicarboxylate	HMDB
2,4-Pyrrolidinedicarboxylate	HMDB
1-trans-Pyrrolidine-2,4-dicarboxylic acid	HMDB
L-Pyrrolidine-2,4-dicarboxylic acid	HMDB
Pyrrolidine-2,4-dicarboxylic acid, (2R-trans)-isomer	HMDB
L-trans-Pyrrolidine-2,4-dicarboxylic acid	HMDB
PDC-2,4	HMDB
Pyrrolidine-2,4-dicarboxylic acid, (2R-cis)-isomer	HMDB
2,4-Pyrrolidine dicarboxylate	HMDB
L-trans-2,4-Pyrrolidine dicarboxylate	HMDB
Pyrrolidine-2,4-dicarboxylic acid, (2S-cis)-isomer	HMDB
1-Pyrrolidine-2,4-dicarboxylic acid	HMDB
Pyrrolidine-2,4-dicarboxylic acid	HMDB
Pyrrolidine-2,4-dicarboxylic acid, (2S-trans)-isomer	HMDB

Chemical Formula

C₆H₉NO₄

Average Molecular Weight

159.141

Monoisotopic Molecular Weight

159.053157774

IUPAC Name

pyrrolidine-2,4-dicarboxylic acid

Traditional Name

pyrrolidine-2,4-dicarboxylic acid

CAS Registry Number

Not Available

SMILES

OC(=O)C1CNC(C1)C(O)=O

InChI Identifier

InChI=1S/C6H9NO4/c8-5(9)3-1-4(6(10)11)7-2-3/h3-4,7H,1-2H2,(H,8,9)(H,10,11)

InChI Key

NRSBQSJHFYZIPH-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as proline and derivatives. Proline and derivatives are compounds containing proline or a derivative thereof resulting from reaction of proline at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Proline and derivatives

Alternative Parents

Substituents

Proline or derivatives
Alpha-amino acid
Pyrrolidine carboxylic acid
Pyrrolidine carboxylic acid or derivatives
Dicarboxylic acid or derivatives
Pyrrolidine
Amino acid
Azacycle
Organoheterocyclic compound
Secondary amine
Secondary aliphatic amine
Carboxylic acid
Organic oxide
Organopnictogen compound
Organooxygen compound
Organonitrogen compound
Organic oxygen compound
Carbonyl group
Amine
Organic nitrogen compound
Hydrocarbon derivative
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic 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	-2.8	ALOGPS
logP	-3.3	ChemAxon
logS	-0.24	ALOGPS
pKa (Strongest Acidic)	1.38	ChemAxon
pKa (Strongest Basic)	11.24	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	86.63 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	34.15 m³·mol⁻¹	ChemAxon
Polarizability	14.27 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

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M+H]+	130.663	30932474
DeepCCS	[M-H]-	126.919	30932474
DeepCCS	[M-2H]-	164.122	30932474
DeepCCS	[M+Na]+	139.422	30932474
AllCCS	[M+H]+	134.5	32859911
AllCCS	[M+H-H2O]+	130.2	32859911
AllCCS	[M+NH4]+	138.6	32859911
AllCCS	[M+Na]+	139.7	32859911
AllCCS	[M-H]-	130.0	32859911
AllCCS	[M+Na-2H]-	131.4	32859911
AllCCS	[M+HCOO]-	132.9	32859911

Predicted Kovats Retention Indices

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
(2R,4S)-Pyrrolidine-2,4-dicarboxylic acid,2TMS,isomer #1	C[Si](C)(C)OC(=O)C1CNC(C(=O)O[Si](C)(C)C)C1	1625.6	Semi standard non polar	33892256
(2R,4S)-Pyrrolidine-2,4-dicarboxylic acid,2TMS,isomer #1	C[Si](C)(C)OC(=O)C1CNC(C(=O)O[Si](C)(C)C)C1	1713.5	Standard non polar	33892256
(2R,4S)-Pyrrolidine-2,4-dicarboxylic acid,2TMS,isomer #1	C[Si](C)(C)OC(=O)C1CNC(C(=O)O[Si](C)(C)C)C1	2220.7	Standard polar	33892256
(2R,4S)-Pyrrolidine-2,4-dicarboxylic acid,2TMS,isomer #3	C[Si](C)(C)OC(=O)C1CC(C(=O)O)CN1[Si](C)(C)C	1675.5	Semi standard non polar	33892256
(2R,4S)-Pyrrolidine-2,4-dicarboxylic acid,2TMS,isomer #3	C[Si](C)(C)OC(=O)C1CC(C(=O)O)CN1[Si](C)(C)C	1672.9	Standard non polar	33892256
(2R,4S)-Pyrrolidine-2,4-dicarboxylic acid,2TMS,isomer #3	C[Si](C)(C)OC(=O)C1CC(C(=O)O)CN1[Si](C)(C)C	2095.8	Standard polar	33892256
(2R,4S)-Pyrrolidine-2,4-dicarboxylic acid,3TMS,isomer #1	C[Si](C)(C)OC(=O)C1CC(C(=O)O[Si](C)(C)C)N([Si](C)(C)C)C1	1693.5	Semi standard non polar	33892256
(2R,4S)-Pyrrolidine-2,4-dicarboxylic acid,3TMS,isomer #1	C[Si](C)(C)OC(=O)C1CC(C(=O)O[Si](C)(C)C)N([Si](C)(C)C)C1	1745.3	Standard non polar	33892256
(2R,4S)-Pyrrolidine-2,4-dicarboxylic acid,3TMS,isomer #1	C[Si](C)(C)OC(=O)C1CC(C(=O)O[Si](C)(C)C)N([Si](C)(C)C)C1	1850.2	Standard polar	33892256
(2R,4S)-Pyrrolidine-2,4-dicarboxylic acid,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC(=O)C1CC(C(=O)O)CN1	1871.7	Semi standard non polar	33892256
(2R,4S)-Pyrrolidine-2,4-dicarboxylic acid,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC(=O)C1CC(C(=O)O)CN1	1821.3	Standard non polar	33892256
(2R,4S)-Pyrrolidine-2,4-dicarboxylic acid,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC(=O)C1CC(C(=O)O)CN1	2776.4	Standard polar	33892256
(2R,4S)-Pyrrolidine-2,4-dicarboxylic acid,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC(=O)C1CC(C(=O)O)N([Si](C)(C)C(C)(C)C)C1	2184.9	Semi standard non polar	33892256
(2R,4S)-Pyrrolidine-2,4-dicarboxylic acid,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC(=O)C1CC(C(=O)O)N([Si](C)(C)C(C)(C)C)C1	2103.6	Standard non polar	33892256
(2R,4S)-Pyrrolidine-2,4-dicarboxylic acid,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC(=O)C1CC(C(=O)O)N([Si](C)(C)C(C)(C)C)C1	2319.3	Standard polar	33892256
(2R,4S)-Pyrrolidine-2,4-dicarboxylic acid,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)C1CC(C(=O)O[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)C1	2386.8	Semi standard non polar	33892256
(2R,4S)-Pyrrolidine-2,4-dicarboxylic acid,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)C1CC(C(=O)O[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)C1	2365.0	Standard non polar	33892256
(2R,4S)-Pyrrolidine-2,4-dicarboxylic acid,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)C1CC(C(=O)O[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)C1	2272.6	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - (2R,4S)-Pyrrolidine-2,4-dicarboxylic acid GC-MS (Non-derivatized) - 70eV, Positive	splash10-029f-9400000000-4fb93bd954975e2bcb97	2021-09-23	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (2R,4S)-Pyrrolidine-2,4-dicarboxylic acid GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (2R,4S)-Pyrrolidine-2,4-dicarboxylic acid GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (2R,4S)-Pyrrolidine-2,4-dicarboxylic acid GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (2R,4S)-Pyrrolidine-2,4-dicarboxylic acid GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (2R,4S)-Pyrrolidine-2,4-dicarboxylic acid GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (2R,4S)-Pyrrolidine-2,4-dicarboxylic acid GC-MS (TMS_1_3) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (2R,4S)-Pyrrolidine-2,4-dicarboxylic acid GC-MS (TMS_2_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (2R,4S)-Pyrrolidine-2,4-dicarboxylic acid GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (2R,4S)-Pyrrolidine-2,4-dicarboxylic acid GC-MS (TBDMS_1_3) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (2R,4S)-Pyrrolidine-2,4-dicarboxylic acid GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (2R,4S)-Pyrrolidine-2,4-dicarboxylic acid GC-MS (TBDMS_2_3) - 70eV, Positive	Not Available	2021-11-03	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 - (2R,4S)-Pyrrolidine-2,4-dicarboxylic acid 10V, Negative-QTOF	splash10-06r6-1900000000-83742f1751c509b190fb	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (2R,4S)-Pyrrolidine-2,4-dicarboxylic acid 20V, Negative-QTOF	splash10-00kb-9200000000-a99b399009257c2cf2fc	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (2R,4S)-Pyrrolidine-2,4-dicarboxylic acid 40V, Negative-QTOF	splash10-0076-9000000000-cc116ff88362b9be1fe3	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (2R,4S)-Pyrrolidine-2,4-dicarboxylic acid 10V, Positive-QTOF	splash10-0007-7900000000-089a32232de292aa4211	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (2R,4S)-Pyrrolidine-2,4-dicarboxylic acid 20V, Positive-QTOF	splash10-014i-9200000000-ae429f095e712b9d4fc7	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (2R,4S)-Pyrrolidine-2,4-dicarboxylic acid 40V, Positive-QTOF	splash10-014i-9000000000-2666d02d34577e76948e	2021-10-12	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	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

3733

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

3868

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 (2R,4S)-Pyrrolidine-2,4-dicarboxylic acid (HMDB0242583)

MOL for HMDB0242583 ((2R,4S)-Pyrrolidine-2,4-dicarboxylic acid)

3D MOL for HMDB0242583 ((2R,4S)-Pyrrolidine-2,4-dicarboxylic acid)

3D SDF for HMDB0242583 ((2R,4S)-Pyrrolidine-2,4-dicarboxylic acid)

3D-SDF for HMDB0242583 ((2R,4S)-Pyrrolidine-2,4-dicarboxylic acid)

PDB for HMDB0242583 ((2R,4S)-Pyrrolidine-2,4-dicarboxylic acid)

3D PDB for HMDB0242583 ((2R,4S)-Pyrrolidine-2,4-dicarboxylic acid)

SMILES for HMDB0242583 ((2R,4S)-Pyrrolidine-2,4-dicarboxylic acid)

INCHI for HMDB0242583 ((2R,4S)-Pyrrolidine-2,4-dicarboxylic acid)

Structure for HMDB0242583 ((2R,4S)-Pyrrolidine-2,4-dicarboxylic acid)

3D Structure for HMDB0242583 ((2R,4S)-Pyrrolidine-2,4-dicarboxylic acid)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra