D-Proline (YMDB00903)

Identification

YMDB ID

YMDB00903

Name

D-Proline

Species

Saccharomyces cerevisiae

Strain

Baker's yeast

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 the action of the enzyme D-amino-acid oxidase. In yeast, D-proline is involved in the metabolic pathway called the arginine and proline metabolism pathway. D-Proline is a potentially toxic compound.

Structure

MOL SDF 3D-SDF PDB SMILES InChI View 3D Structure

Synonyms

(2R)-pyrrolidine-2-carboxylate
(2R)-pyrrolidine-2-carboxylic acid
(R)-pyrrolidine-2-carboxylate
(R)-pyrrolidine-2-carboxylic acid
D-Prolin
D-proline
R-Proline
R)-2-Carboxypyrrolidine
(R)-2-Carboxypyrrolidine
DPR
Proline

CAS number

344-25-2

Weight

Average: 115.1305
Monoisotopic: 115.063328537

InChI Key

ONIBWKKTOPOVIA-SCSAIBSYSA-N

InChI

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

IUPAC Name

(2R)-pyrrolidine-2-carboxylic acid

Traditional IUPAC Name

D-proline

Chemical Formula

C₅H₉NO₂

SMILES

[H]OC(=O)[C@]1([H])N([H])C([H])([H])C([H])([H])C1([H])[H]

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 )

Physical Properties

State

Solid

Charge

Melting point

221 °C

Experimental Properties

Property	Value	Reference
Water Solubility	162 mg/mL at 25 oC [MERCK INDEX (1996)]	PhysProp
LogP	-2.54 [HANSCH,C ET AL. (1995)]	PhysProp

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	1	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations

Not Available

Organoleptic Properties

Not Available

SMPDB Pathways

Not Available

KEGG Pathways

Arginine and proline metabolism

ec00330

SMPDB Reactions

Not Available

KEGG Reactions

Not Available

Concentrations

Intracellular Concentrations

Not Available

Extracellular Concentrations

Not Available

Spectra

Spectrum Type	Description	Splash Key	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-00fu-9000000000-d203e3dfb0701403a75b	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	splash10-00di-9000000000-56471980a375d26046ca	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	JSpectraViewer
LC-MS/MS	LC-MS/MS Spectrum - 20V, Positive	splash10-00di-9000000000-d3689ce7d1b666093d7f	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - 10V, Positive	splash10-00di-9200000000-0ff57624fa424cf13f20	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - 10V, Negative	splash10-03di-3900000000-01469d0f80dcbecd0185	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - 40V, Positive	splash10-00di-9000000000-b429bf31961274bc04e3	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - 20V, Negative	splash10-0bt9-9600000000-5d761bf19a4ea84edc9c	JSpectraViewer \| MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-014i-6900000000-eba8ceb2a71d2726acd0	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-00di-9200000000-c52871a4097a833a301a	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-006x-9000000000-50a811fa0506a025048a	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-03di-3900000000-ba371efbf747c7eed1a7	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-03k9-9600000000-f8a0815fbf4d1b2713af	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9000000000-133753f87329f1da7d39	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-03di-3900000000-2d7e8539e5f8306d0afe	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-01ot-9400000000-b7d551a4cee7688ee082	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9000000000-a4e2ca2cba04978b1bf6	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-00di-9000000000-97990d3a6f4d86f2e35e	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-00di-9000000000-6af75747a42ba65860f4	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-00di-9000000000-4d5b790a456b8349d65b	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer

References

References:

Scheer, M., Grote, A., Chang, A., Schomburg, I., Munaretto, C., Rother, M., Sohngen, C., Stelzer, M., Thiele, J., Schomburg, D. (2011). "BRENDA, the enzyme information system in 2011." Nucleic Acids Res 39:D670-D676.21062828
Horak, J., Rihova, L. (1982). "L-Proline transport in Saccharomyces cerevisiae." Biochim Biophys Acta 691:144-150.6753931

Synthesis Reference:

Not Available

External Links:

Resource	Link
CHEBI ID	16313
HMDB ID	HMDB03411
Pubchem Compound ID	8988
Kegg ID	C00763
ChemSpider ID	8640
FOODB ID	FDB023166
Wikipedia	Proline
BioCyc ID	CPD-656

Enzymes

Protein Details

1. N-acetyltransferase HPA3

General function:: Involved in N-acetyltransferase activity
Specific function:: N-acetyltransferase whose physiological acetyl acceptor substrate is still unknown. In vitro, histone acetylation is very weak
Gene Name:: HPA3
Uniprot ID:: P39979
Molecular weight:: 20698.5

Reactions

acetyl-CoA + a D-amino acid → CoA + an N-acetyl-D-amino acid

Structure for #<Compound:0x9a951f74>

Enzymes

Reactions