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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (2) Show 2 proteins XML

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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2006-08-12 20:18:30 UTC

Update Date

2022-03-07 02:49:18 UTC

HMDB ID

HMDB0003411

Secondary Accession Numbers

HMDB03411

Metabolite Identification

Common Name

D-Proline

Description

D-Proline, also known as D-prolin or DPR, 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. D-Proline is a very strong basic compound (based on its pKa). D-Proline exists in all living species, ranging from bacteria to humans. D-proline can be converted into 1-pyrroline-2-carboxylic acid through its interaction with the enzyme D-amino-acid oxidase. In humans, D-proline is involved in the metabolic disorder called hyperornithinemia with gyrate atrophy (hoga). D-Proline is a potentially toxic compound. The D-enantiomer of proline.

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)-Pyrrolidine-2-carboxylic acid	ChEBI
(R)-2-Carboxypyrrolidine	ChEBI
(R)-Pyrrolidine-2-carboxylic acid	ChEBI
D-Prolin	ChEBI
DPR	ChEBI
(2R)-Pyrrolidine-2-carboxylate	Generator
(R)-Pyrrolidine-2-carboxylate	Generator
R)-2-Carboxypyrrolidine	HMDB
R-Proline	HMDB
Proline	HMDB

Chemical Formula

C₅H₉NO₂

Average Molecular Weight

115.1305

Monoisotopic Molecular Weight

115.063328537

IUPAC Name

(2R)-pyrrolidine-2-carboxylic acid

Traditional Name

D-proline

CAS Registry Number

344-25-2

SMILES

OC(=O)[C@H]1CCCN1

InChI Identifier

InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/t4-/m1/s1

InChI Key

ONIBWKKTOPOVIA-SCSAIBSYSA-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
D-alpha-amino acid
Pyrrolidine carboxylic acid
Pyrrolidine carboxylic acid or derivatives
Pyrrolidine
Amino acid
Carboxylic acid
Secondary aliphatic amine
Monocarboxylic acid or derivatives
Secondary amine
Organoheterocyclic compound
Azacycle
Organic oxygen compound
Organooxygen compound
Organonitrogen compound
Amine
Organopnictogen compound
Organic oxide
Carbonyl group
Organic nitrogen compound
Hydrocarbon derivative
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

D-alpha-amino acid (CHEBI:16313 )
proline (CHEBI:16313 )
Other amino acids (C00763 )

Ontology

Not Available

Urine (PMID: 21389975)

Cellular substructure

Extracellular (HMDB: HMDB0003411)
Membrane (HMDB: HMDB0003411)

Organelle

Lysosome (HMDB: HMDB0003411)
Peroxisome (HMDB: HMDB0003411)

Non-excretory biofluid

Biofluid or Excreta

Blood (HMDB: HMDB0003411)

Source

Exogenous

Exogenous (HMDB: HMDB0003411)

Food

Animal origin

Poultry

Pheasant (FooDB: FOOD00430)
Squab (FooDB: FOOD00481)
Turkey (FooDB: FOOD00494)
Quail (FooDB: FOOD00541)
Anatidae (FooDB: FOOD00576)
Rock ptarmigan (FooDB: FOOD00597)
Columbidae (Dove, Pigeon) (FooDB: FOOD00610)
Chicken (FooDB: FOOD00329)
Mallard duck (FooDB: FOOD00353)
Emu (FooDB: FOOD00360)
Greylag goose (FooDB: FOOD00368)
Guinea hen (FooDB: FOOD00373)
Ostrich (FooDB: FOOD00422)
Velvet duck (FooDB: FOOD00427)

Lagomorph

Ovis

Sheep (Mutton, Lamb) (FooDB: FOOD00473)

Bovine

Venison

Deer (FooDB: FOOD00524)
Mule deer (FooDB: FOOD00348)
Elk (FooDB: FOOD00359)

Caprae

Domestic goat (FooDB: FOOD00529)

Swine

Domestic pig (FooDB: FOOD00536)
Wild boar (FooDB: FOOD00307)

Equine

Horse (FooDB: FOOD00378)

Endogenous

Endogenous (HMDB: HMDB0003411)

Microbe

Microbe (HMDB: HMDB0003411)

Process

Naturally occurring process

Biological process

Biochemical pathway

Metabolic pathway

Arginine and Proline Metabolism (HMDB: HMDB0003411)
Arginine and Proline Metabolism (HMDB: HMDB0003411)

Disease pathway

Role

Industrial application

Pharmaceutical industry

Pharmaceutical (HMDB: HMDB0003411)

Biological role

Human metabolite (HMDB: HMDB0003411)

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	221 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct Type	Data Source	CCS Value (Å²)	Reference
[M-H]-	MetCCS_train_neg	122.49	30932474
[M+H]+	MetCCS_train_pos	125.048	30932474
[M-H]-	Not Available	122.49	http://allccs.zhulab.cn/database/detail?ID=AllCCS00000058
[M+H]+	Not Available	124.949	http://allccs.zhulab.cn/database/detail?ID=AllCCS00000058

Predicted Molecular Properties

Property	Value	Source
Water Solubility	365 g/L	ALOGPS
logP	-2.7	ALOGPS
logP	-2.6	ChemAxon
logS	0.5	ALOGPS
pKa (Strongest Acidic)	1.94	ChemAxon
pKa (Strongest Basic)	11.33	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	49.33 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	28.06 m³·mol⁻¹	ChemAxon
Polarizability	11.39 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
DarkChem	[M+H]+	124.064	31661259
DarkChem	[M-H]-	118.832	31661259
DeepCCS	[M+H]+	118.57	30932474
DeepCCS	[M-H]-	114.922	30932474
DeepCCS	[M-2H]-	152.317	30932474
DeepCCS	[M+Na]+	127.301	30932474
AllCCS	[M+H]+	125.1	32859911
AllCCS	[M+H-H2O]+	120.3	32859911
AllCCS	[M+NH4]+	129.5	32859911
AllCCS	[M+Na]+	130.8	32859911
AllCCS	[M-H]-	120.9	32859911
AllCCS	[M+Na-2H]-	123.4	32859911
AllCCS	[M+HCOO]-	126.2	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
D-Proline	OC(=O)[C@H]1CCCN1	1823.6	Standard polar	33892256
D-Proline	OC(=O)[C@H]1CCCN1	1083.3	Standard non polar	33892256
D-Proline	OC(=O)[C@H]1CCCN1	1293.2	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
D-Proline,1TMS,isomer #1	C[Si](C)(C)OC(=O)[C@H]1CCCN1	1178.4	Semi standard non polar	33892256
D-Proline,1TMS,isomer #2	C[Si](C)(C)N1CCC[C@@H]1C(=O)O	1275.7	Semi standard non polar	33892256
D-Proline,2TMS,isomer #1	C[Si](C)(C)OC(=O)[C@H]1CCCN1[Si](C)(C)C	1311.0	Semi standard non polar	33892256
D-Proline,2TMS,isomer #1	C[Si](C)(C)OC(=O)[C@H]1CCCN1[Si](C)(C)C	1357.1	Standard non polar	33892256
D-Proline,2TMS,isomer #1	C[Si](C)(C)OC(=O)[C@H]1CCCN1[Si](C)(C)C	1555.9	Standard polar	33892256
D-Proline,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)[C@H]1CCCN1	1420.9	Semi standard non polar	33892256
D-Proline,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N1CCC[C@@H]1C(=O)O	1551.5	Semi standard non polar	33892256
D-Proline,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)[C@H]1CCCN1[Si](C)(C)C(C)(C)C	1769.8	Semi standard non polar	33892256
D-Proline,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)[C@H]1CCCN1[Si](C)(C)C(C)(C)C	1775.0	Standard non polar	33892256
D-Proline,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)[C@H]1CCCN1[Si](C)(C)C(C)(C)C	1834.0	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - D-Proline GC-MS (Non-derivatized) - 70eV, Positive	splash10-00fu-9000000000-d203e3dfb0701403a75b	2016-09-22	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - D-Proline GC-MS (1 TMS) - 70eV, Positive	splash10-00di-9000000000-56471980a375d26046ca	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - D-Proline 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
Experimental LC-MS/MS	LC-MS/MS Spectrum - D-Proline 20V, Positive-QTOF	splash10-00di-9000000000-d3689ce7d1b666093d7f	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - D-Proline 10V, Positive-QTOF	splash10-00di-9200000000-0ff57624fa424cf13f20	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - D-Proline 10V, Negative-QTOF	splash10-03di-3900000000-01469d0f80dcbecd0185	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - D-Proline 40V, Positive-QTOF	splash10-00di-9000000000-b429bf31961274bc04e3	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - D-Proline 20V, Negative-QTOF	splash10-0bt9-9600000000-5d761bf19a4ea84edc9c	2021-09-20	HMDB team, MONA	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Proline 10V, Positive-QTOF	splash10-014i-6900000000-eba8ceb2a71d2726acd0	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Proline 20V, Positive-QTOF	splash10-00di-9200000000-c52871a4097a833a301a	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Proline 40V, Positive-QTOF	splash10-006x-9000000000-50a811fa0506a025048a	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Proline 10V, Negative-QTOF	splash10-03di-3900000000-ba371efbf747c7eed1a7	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Proline 20V, Negative-QTOF	splash10-03k9-9600000000-f8a0815fbf4d1b2713af	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Proline 40V, Negative-QTOF	splash10-0006-9000000000-133753f87329f1da7d39	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Proline 10V, Negative-QTOF	splash10-03di-3900000000-2d7e8539e5f8306d0afe	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Proline 20V, Negative-QTOF	splash10-01ot-9400000000-b7d551a4cee7688ee082	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Proline 40V, Negative-QTOF	splash10-0006-9000000000-a4e2ca2cba04978b1bf6	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Proline 10V, Positive-QTOF	splash10-00di-9000000000-97990d3a6f4d86f2e35e	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Proline 20V, Positive-QTOF	splash10-00di-9000000000-6af75747a42ba65860f4	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Proline 40V, Positive-QTOF	splash10-00di-9000000000-4d5b790a456b8349d65b	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)	2021-09-24	Wishart Lab	View Spectrum
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, 1000 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, 200 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, 300 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, 400 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, 500 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, 600 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, 700 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, 800 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, 900 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

Biological Properties

Cellular Locations

Extracellular
Lysosome
Peroxisome

Biospecimen Locations

Urine

Tissue Locations

Not Available

Pathways

Name	SMPDB/PathBank	KEGG
Arginine and proline metabolism	Not Available
Prolidase Deficiency (PD)		Not Available
Arginine: Glycine Amidinotransferase Deficiency (AGAT Deficiency)		Not Available
Hyperprolinemia Type II		Not Available
Hyperprolinemia Type I		Not Available

Normal Concentrations

Not Available

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Urine	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Autosomal dominant polycystic kidney disease (ADPKD)	21389975	details

Associated Disorders and Diseases

Disease References

Autosomal dominant polycystic kidney disease
Gronwald W, Klein MS, Zeltner R, Schulze BD, Reinhold SW, Deutschmann M, Immervoll AK, Boger CA, Banas B, Eckardt KU, Oefner PJ: Detection of autosomal dominant polycystic kidney disease by NMR spectroscopic fingerprinting of urine. Kidney Int. 2011 Jun;79(11):1244-53. doi: 10.1038/ki.2011.30. Epub 2011 Mar 9. [PubMed:21389975 ]

Associated OMIM IDs

601313 (Autosomal dominant polycystic kidney disease)

External Links

DrugBank ID

DB02853

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB023166

KNApSAcK ID

Not Available

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Wikipedia Link

METLIN ID

Not Available

PubChem Compound

8988

PDB ID

Not Available

ChEBI ID

16313

Food Biomarker Ontology

Not Available

VMH ID

PRO_D

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

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Enzymes

Enzyme Details

1. D-amino-acid oxidase

General function:: Involved in D-amino-acid oxidase activity
Specific function:: Regulates the level of the neuromodulator D-serine in the brain. Has high activity towards D-DOPA and contributes to dopamine synthesis. Could act as a detoxifying agent which removes D-amino acids accumulated during aging. Acts on a variety of D-amino acids with a preference for those having small hydrophobic side chains followed by those bearing polar, aromatic, and basic groups. Does not act on acidic amino acids.
Gene Name:: DAO
Uniprot ID:: P14920
Molecular weight:: 39473.75

Reactions

D-Proline + Oxygen → 1-Pyrroline-2-carboxylic acid + Hydrogen peroxide	details

Enzyme Details

2. Trans-L-3-hydroxyproline dehydratase

General function:: Involved in proline racemase activity
Specific function:: Catalyzes the dehydration of trans-3-hydroxy-L-proline to delta-1-pyrroline-2-carboxylate (Pyr2C). May be required to degrade trans-3-hydroxy-L-proline from the diet and originating from the degradation of proteins such as collagen-IV that contain it.
Gene Name:: L3HYPDH
Uniprot ID:: Q96EM0
Molecular weight:: 38137.395

Showing metabocard for D-Proline (HMDB0003411)

MOL for HMDB0003411 (D-Proline)

3D MOL for HMDB0003411 (D-Proline)

3D SDF for HMDB0003411 (D-Proline)

3D-SDF for HMDB0003411 (D-Proline)

PDB for HMDB0003411 (D-Proline)

3D PDB for HMDB0003411 (D-Proline)

SMILES for HMDB0003411 (D-Proline)

INCHI for HMDB0003411 (D-Proline)

Structure for HMDB0003411 (D-Proline)

3D Structure for HMDB0003411 (D-Proline)

Experimental Collision Cross Sections

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

Enzymes

Reactions