Jump To Section:

Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (1) Show 1 protein XML

Show more...Show more...Show more...

Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2013-05-17 01:22:22 UTC

Update Date

2023-02-21 17:30:01 UTC

HMDB ID

HMDB0060460

Secondary Accession Numbers

HMDB60460

Metabolite Identification

Common Name

cis-4-Hydroxy-D-proline

Description

cis-4-Hydroxy-D-proline 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. cis-4-Hydroxy-D-proline is a very strong basic compound (based on its pKa). cis-4-Hydroxy-D-proline exists in all living organisms, ranging from bacteria to humans. A 4-hydroxy-D-proline in which the hydroxy group at position 4 has R-configuration.

Structure

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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₅H₉NO₃

Average Molecular Weight

131.1299

Monoisotopic Molecular Weight

131.058243159

IUPAC Name

(2R,4R)-4-hydroxypyrrolidine-2-carboxylic acid

Traditional Name

cis-4-hydroxy-D-proline

CAS Registry Number

2584-71-6

SMILES

O[C@H]1CN[C@H](C1)C(O)=O

InChI Identifier

InChI=1S/C5H9NO3/c7-3-1-4(5(8)9)6-2-3/h3-4,6-7H,1-2H2,(H,8,9)/t3-,4-/m1/s1

InChI Key

PMMYEEVYMWASQN-QWWZWVQMSA-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
1,2-aminoalcohol
Amino acid
Secondary alcohol
Carboxylic acid
Secondary aliphatic amine
Monocarboxylic acid or derivatives
Azacycle
Secondary amine
Organoheterocyclic compound
Organooxygen compound
Organonitrogen compound
Alcohol
Organic nitrogen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organic oxygen compound
Amine
Carbonyl group
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

4-hydroxyproline (CHEBI:16231 )

Ontology

Not Available

Exogenous (HMDB: HMDB0060460)

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

Experimental Collision Cross Sections

Adduct Type	Data Source	CCS Value (Å²)	Reference
[M-H]-	MetCCS_train_neg	122.024	30932474
[M+H]+	MetCCS_train_pos	128.374	30932474

Predicted Molecular Properties

Property	Value	Source
Water Solubility	492 g/L	ALOGPS
logP	-3.3	ALOGPS
logP	-3.7	ChemAxon
logS	0.57	ALOGPS
pKa (Strongest Acidic)	1.64	ChemAxon
pKa (Strongest Basic)	10.62	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	69.56 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	29.38 m³·mol⁻¹	ChemAxon
Polarizability	12.34 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]+	126.14	31661259
DarkChem	[M-H]-	123.52	31661259
DeepCCS	[M+H]+	125.335	30932474
DeepCCS	[M-H]-	121.73	30932474
DeepCCS	[M-2H]-	159.094	30932474
DeepCCS	[M+Na]+	134.512	30932474
AllCCS	[M+H]+	129.1	32859911
AllCCS	[M+H-H2O]+	124.5	32859911
AllCCS	[M+NH4]+	133.4	32859911
AllCCS	[M+Na]+	134.7	32859911
AllCCS	[M-H]-	123.0	32859911
AllCCS	[M+Na-2H]-	125.1	32859911
AllCCS	[M+HCOO]-	127.4	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
cis-4-Hydroxy-D-proline	O[C@H]1CN[C@H](C1)C(O)=O	2552.8	Standard polar	33892256
cis-4-Hydroxy-D-proline	O[C@H]1CN[C@H](C1)C(O)=O	1284.4	Standard non polar	33892256
cis-4-Hydroxy-D-proline	O[C@H]1CN[C@H](C1)C(O)=O	1552.1	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
cis-4-Hydroxy-D-proline,1TMS,isomer #1	C[Si](C)(C)O[C@H]1CN[C@@H](C(=O)O)C1	1449.4	Semi standard non polar	33892256
cis-4-Hydroxy-D-proline,1TMS,isomer #2	C[Si](C)(C)OC(=O)[C@H]1C[C@@H](O)CN1	1354.4	Semi standard non polar	33892256
cis-4-Hydroxy-D-proline,1TMS,isomer #3	C[Si](C)(C)N1C[C@H](O)C[C@@H]1C(=O)O	1432.0	Semi standard non polar	33892256
cis-4-Hydroxy-D-proline,2TMS,isomer #1	C[Si](C)(C)OC(=O)[C@H]1C[C@@H](O[Si](C)(C)C)CN1	1442.1	Semi standard non polar	33892256
cis-4-Hydroxy-D-proline,2TMS,isomer #2	C[Si](C)(C)O[C@@H]1C[C@H](C(=O)O)N([Si](C)(C)C)C1	1471.9	Semi standard non polar	33892256
cis-4-Hydroxy-D-proline,2TMS,isomer #3	C[Si](C)(C)OC(=O)[C@H]1C[C@@H](O)CN1[Si](C)(C)C	1442.8	Semi standard non polar	33892256
cis-4-Hydroxy-D-proline,3TMS,isomer #1	C[Si](C)(C)OC(=O)[C@H]1C[C@@H](O[Si](C)(C)C)CN1[Si](C)(C)C	1500.8	Semi standard non polar	33892256
cis-4-Hydroxy-D-proline,3TMS,isomer #1	C[Si](C)(C)OC(=O)[C@H]1C[C@@H](O[Si](C)(C)C)CN1[Si](C)(C)C	1594.0	Standard non polar	33892256
cis-4-Hydroxy-D-proline,3TMS,isomer #1	C[Si](C)(C)OC(=O)[C@H]1C[C@@H](O[Si](C)(C)C)CN1[Si](C)(C)C	1683.5	Standard polar	33892256
cis-4-Hydroxy-D-proline,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)O[C@H]1CN[C@@H](C(=O)O)C1	1682.0	Semi standard non polar	33892256
cis-4-Hydroxy-D-proline,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC(=O)[C@H]1C[C@@H](O)CN1	1602.4	Semi standard non polar	33892256
cis-4-Hydroxy-D-proline,1TBDMS,isomer #3	CC(C)(C)[Si](C)(C)N1C[C@H](O)C[C@@H]1C(=O)O	1698.2	Semi standard non polar	33892256
cis-4-Hydroxy-D-proline,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)[C@H]1C[C@@H](O[Si](C)(C)C(C)(C)C)CN1	1905.5	Semi standard non polar	33892256
cis-4-Hydroxy-D-proline,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)O[C@@H]1C[C@H](C(=O)O)N([Si](C)(C)C(C)(C)C)C1	1989.8	Semi standard non polar	33892256
cis-4-Hydroxy-D-proline,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC(=O)[C@H]1C[C@@H](O)CN1[Si](C)(C)C(C)(C)C	1919.3	Semi standard non polar	33892256
cis-4-Hydroxy-D-proline,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)[C@H]1C[C@@H](O[Si](C)(C)C(C)(C)C)CN1[Si](C)(C)C(C)(C)C	2197.5	Semi standard non polar	33892256
cis-4-Hydroxy-D-proline,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)[C@H]1C[C@@H](O[Si](C)(C)C(C)(C)C)CN1[Si](C)(C)C(C)(C)C	2189.9	Standard non polar	33892256
cis-4-Hydroxy-D-proline,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)[C@H]1C[C@@H](O[Si](C)(C)C(C)(C)C)CN1[Si](C)(C)C(C)(C)C	2100.8	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - cis-4-Hydroxy-D-proline GC-MS (Non-derivatized) - 70eV, Positive	splash10-07g3-9100000000-7e4ece693ce885f2589c	2017-09-20	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - cis-4-Hydroxy-D-proline GC-MS (2 TMS) - 70eV, Positive	splash10-0a4i-5910000000-8b634c853b803e2ce4d3	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - cis-4-Hydroxy-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 - cis-4-Hydroxy-D-proline 35V, Negative-QTOF	splash10-001i-1900000000-d67cfd972ed1b98aa9e3	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - cis-4-Hydroxy-D-proline 10V, Negative-QTOF	splash10-001i-1900000000-2b0877cf0410f0d2cd41	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - cis-4-Hydroxy-D-proline 35V, Positive-QTOF	splash10-000i-9300000000-05ad909ac50d5e470e11	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - cis-4-Hydroxy-D-proline 35V, Positive-QTOF	splash10-000i-9300000000-7c512947e6be87aef211	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - cis-4-Hydroxy-D-proline 10V, Positive-QTOF	splash10-000i-9100000000-d3fcd8a4b48adae5bf8e	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - cis-4-Hydroxy-D-proline 20V, Positive-QTOF	splash10-00kr-9000000000-a96046f5413dad11b39d	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - cis-4-Hydroxy-D-proline 40V, Positive-QTOF	splash10-014l-9000000000-e48c667ac1efe0e9e493	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - cis-4-Hydroxy-D-proline 10V, Positive-QTOF	splash10-000i-9100000000-936506fab96eade9a3ba	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - cis-4-Hydroxy-D-proline 40V, Positive-QTOF	splash10-066u-9000000000-d26e8bc8fc518d2dfb00	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - cis-4-Hydroxy-D-proline 20V, Positive-QTOF	splash10-00kr-9000000000-2a6c5f880195b2c7d467	2021-09-20	HMDB team, MONA	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - cis-4-Hydroxy-D-proline 10V, Positive-QTOF	splash10-03di-3900000000-54b8ac52a265772761b5	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - cis-4-Hydroxy-D-proline 20V, Positive-QTOF	splash10-02t9-9400000000-8302666cfee04dd777ff	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - cis-4-Hydroxy-D-proline 40V, Positive-QTOF	splash10-014l-9000000000-94ec52ef1a3baca29ced	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - cis-4-Hydroxy-D-proline 10V, Negative-QTOF	splash10-001i-2900000000-276917674ec7e7c3d6db	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - cis-4-Hydroxy-D-proline 20V, Negative-QTOF	splash10-03yi-7900000000-dbe7a1905f8ee1beda93	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - cis-4-Hydroxy-D-proline 40V, Negative-QTOF	splash10-00kf-9000000000-cec6276d54ed5d3a5424	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - cis-4-Hydroxy-D-proline 10V, Positive-QTOF	splash10-03yr-4900000000-956289a1f2420b73ca3d	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - cis-4-Hydroxy-D-proline 20V, Positive-QTOF	splash10-014i-9100000000-b31bfff7a750b532e918	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - cis-4-Hydroxy-D-proline 40V, Positive-QTOF	splash10-0aou-9000000000-9473acfa9148a036c0ba	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - cis-4-Hydroxy-D-proline 10V, Negative-QTOF	splash10-01q9-3900000000-206002d6953f7b8754ab	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - cis-4-Hydroxy-D-proline 20V, Negative-QTOF	splash10-03y0-9600000000-624dbd787acc76434f16	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - cis-4-Hydroxy-D-proline 40V, Negative-QTOF	splash10-0006-9000000000-73f483e220b16df3a0ab	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)	2021-09-24	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

IR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)	2023-02-04	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)	2023-02-04	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)	2023-02-04	FELIX lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

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

Not Available

KEGG Compound ID

C03440

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

440014

PDB ID

Not Available

ChEBI ID

16231

Food Biomarker Ontology

Not Available

VMH ID

4HPRO_D

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Magrane M: UniProt Knowledgebase: a hub of integrated protein data. Database (Oxford). 2011 Mar 29;2011:bar009. doi: 10.1093/database/bar009. Print 2011. [PubMed:21447597 ]

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

cis-4-Hydroxy-D-proline + Oxygen → 1-Pyrroline-4-hydroxy-2-carboxylate + Hydrogen peroxide	details

Showing metabocard for cis-4-Hydroxy-D-proline (HMDB0060460)

MOL for HMDB0060460 (cis-4-Hydroxy-D-proline)

3D MOL for HMDB0060460 (cis-4-Hydroxy-D-proline)

3D SDF for HMDB0060460 (cis-4-Hydroxy-D-proline)

3D-SDF for HMDB0060460 (cis-4-Hydroxy-D-proline)

PDB for HMDB0060460 (cis-4-Hydroxy-D-proline)

3D PDB for HMDB0060460 (cis-4-Hydroxy-D-proline)

SMILES for HMDB0060460 (cis-4-Hydroxy-D-proline)

INCHI for HMDB0060460 (cis-4-Hydroxy-D-proline)

Structure for HMDB0060460 (cis-4-Hydroxy-D-proline)

3D Structure for HMDB0060460 (cis-4-Hydroxy-D-proline)

Experimental Collision Cross Sections

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra

Enzymes

Reactions