MiMeDB: Showing metabocard for D-Proline (MMDBc0000242)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2020-10-27 23:41:03 UTC

Update Date

2022-08-31 00:16:05 UTC

Metabolite ID

MMDBc0000242

Metabolite Identification

Common Name

D-Proline

Description

D-proline is an isomer of the naturally occurring amino acid, L-Proline. D-amino acids have been found in relatively high abundance in human plasma and saliva (PMID: 16480744 ). These amino acids may be of bacterial origin, but there is also evidence that they are endogenously produced through amino acid racemase activity (PMID: 1426150 ).

Structure

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

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

Molecular Formula

C₅H₉NO₂

Average Mass

115.1305

Monoisotopic Mass

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 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted 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

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-00fu-9000000000-d203e3dfb0701403a75b	2016-09-22	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	splash10-00di-9000000000-56471980a375d26046ca	2017-10-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 20V, Positive	splash10-00di-9000000000-d3689ce7d1b666093d7f	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 10V, Positive	splash10-00di-9200000000-0ff57624fa424cf13f20	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 10V, Negative	splash10-03di-3900000000-01469d0f80dcbecd0185	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 40V, Positive	splash10-00di-9000000000-b429bf31961274bc04e3	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 20V, Negative	splash10-0bt9-9600000000-5d761bf19a4ea84edc9c	2021-09-20	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-014i-6900000000-eba8ceb2a71d2726acd0	2016-08-03	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-00di-9200000000-c52871a4097a833a301a	2016-08-03	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-006x-9000000000-50a811fa0506a025048a	2016-08-03	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-03di-3900000000-ba371efbf747c7eed1a7	2016-08-03	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-03k9-9600000000-f8a0815fbf4d1b2713af	2016-08-03	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9000000000-133753f87329f1da7d39	2016-08-03	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-03di-3900000000-2d7e8539e5f8306d0afe	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-01ot-9400000000-b7d551a4cee7688ee082	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9000000000-a4e2ca2cba04978b1bf6	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-00di-9000000000-97990d3a6f4d86f2e35e	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-00di-9000000000-6af75747a42ba65860f4	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-00di-9000000000-4d5b790a456b8349d65b	2021-09-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-24	View Spectrum

Biological Properties

Cellular Locations

Extracellular
Lysosome
Peroxisome

Biospecimen Locations

Blood
Urine

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
MMDBp0191877	D-amino-acid oxidase	Unknown	P14920	Homo sapiens
MMDBp0196275	Trans-L-3-hydroxyproline dehydratase	Enzyme	Q96EM0	Homo sapiens

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0000826	Oxygen	1-Pyrroline-2-carboxylic acid	D-amino-acid oxidase	D-Proline Oxidase, Perixosomal	VMH	16141519
MMDBr0002000	Hydrogen Ion	Hydrogen Ion	Solute carrier family 36 (proton/amino acid symporter), member 1	D-Proline Reversible Transport via Proton Symport	VMH	11390972 11959859
MMDBr0002001	Hydrogen Ion	Hydrogen Ion	Solute carrier family 36 (proton/amino acid symporter), member 1	D-Proline Reversible Transport via Proton Symport, Lysosomal	VMH	11390972 11959859
MMDBr0005513	D-Proline	D-Proline	Not Available	D-Proline Transport, Extracellular	VMH	30371894
MMDBr0008182	5-Aminopentanoic acid	Dihydrolipoate	Not Available	5-Aminopentanoate:lipoate oxidoreductase (cyclizing)	VMH	30371894
MMDBr0008198	L-Proline	D-Proline	Not Available	Proline racemase	VMH	30371894
MMDBr0008225	Hydrogen Ion	5-Aminopentanoic acid	Not Available	D-proline reductase	VMH	30371894
MMDBr0008346	Oxygen	1-Pyrroline-2-carboxylic acid	Not Available	Pro-D[c]:oxygen oxidoreductase (deaminating)	VMH	30371894
MMDBr0010647	Oxygen	1-Pyrroline-2-carboxylic acid	D-amino-acid oxidase	D-Amino-Acid Oxidase	VMH	30371894
MMDBr0017835	L-Proline	D-Proline	Proline racemase	Racemization	RHEA	34755880
MMDBr0024428	5-Aminopentanoic acid	L-Cysteine	D-proline reductase proprotein PrdA	Reduction	RHEA	34755880
MMDBr0024818	D-Proline	1-Pyrroline-2-carboxylic acid	D-proline dehydrogenase	Dehydrogenation	RHEA	34755880
MMDBr0026123	Acetyl-CoA	Hydrogen Ion	D-amino-acid N-acetyltransferase HPA3	Acetylation	RHEA	34755880
MMDBr0026129	L-Proline	D-Proline	Broad substrate specificity amino-acid racemase	Racemization	RHEA	34755880
MMDBr0039020	L-Proline	D-Proline	Broad specificity amino-acid racemase	Racemization	RHEA	34755880

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
Eukaryota	Euglenozoa	1		Microbial culture
Bacteria	Deinococcus-thermus	1		Microbial culture
Bacteria	Firmicutes	65	Human ; Human mucosa; Human feces; Human subgingival plaque; Human vaginal secretion; Goat feces; Sheep feces	Microbial culture; Metabolic reconstruction
Bacteria	Proteobacteria	32	Human feces; Human sputum; Human	Microbial culture; Metabolic reconstruction
Bacteria	Bacteroidetes	5	Human feces	Microbial culture; Metabolic reconstruction
Eukaryota	Euglenozoa	2	Goat blood	Microbial culture
Bacteria	Actinobacteria	8	Human feces; Human	Metabolic reconstruction
Bacteria	Synergistetes	1	Human feces	Metabolic reconstruction
Eukaryota/Fungi	Ascomycota	1	Human feces; Human saliva	Unknown

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Urine	Detected but not Quantified						Adult (>18 years old)	Both	Autosomal dominant polycystic kidney disease (ADPKD)	HMDB	21389975
Human Blood	Detected but not Quantified									HMDB

External Links

HMDB ID

HMDB0003411

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

References

Synthesis Reference

Not Available

General References

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Showing metabocard for D-Proline (MMDBc0000242)

MOL for #<Metabolite:0x00007f5a8cf28918>

3D MOL for #<Metabolite:0x00007f5a8cf28918>

3D SDF for #<Metabolite:0x00007f5a8cf28918>

3D-SDF for #<Metabolite:0x00007f5a8cf28918>

PDB for #<Metabolite:0x00007f5a8cf28918>

3D PDB for #<Metabolite:0x00007f5a8cf28918>

SMILES for #<Metabolite:0x00007f5a8cf28918>

INCHI for #<Metabolite:0x00007f5a8cf28918>

Structure for #<Metabolite:0x00007f5a8cf28918>

3D Structure for #<Metabolite:0x00007f5a8cf28918>