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

enzymes (1) Show 1 protein

Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-10-30 10:32:48 UTC

Update Date

2023-02-21 17:29:10 UTC

HMDB ID

HMDB0059659

Secondary Accession Numbers

HMDB59659

Metabolite Identification

Common Name

Trans-3-hydroxy-L-proline

Description

Trans-3-hydroxy-L-proline, also known as L-threo-3-hydroxyproline, 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. Trans-3-hydroxy-L-proline is a very strong basic compound (based on its pKa).

Structure

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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
(2S,3S)-3-Hydroxypyrrolidine-2-carboxylic acid	ChEBI
3-trans-Hydroxy-L-proline	ChEBI
L-Threo-3-hydroxyproline	ChEBI
trans-L-3-Hydroxyproline	ChEBI
(2S,3S)-3-Hydroxypyrrolidine-2-carboxylate	Generator

Chemical Formula

C₅H₉NO₃

Average Molecular Weight

131.1299

Monoisotopic Molecular Weight

131.058243159

IUPAC Name

(2S,3S)-3-hydroxypyrrolidine-2-carboxylic acid

Traditional Name

trans-3-hydroxy-L-proline

CAS Registry Number

Not Available

SMILES

[H][C@]1(O)CCN[C@]1([H])C(O)=O

InChI Identifier

InChI=1S/C5H9NO3/c7-3-1-2-6-4(3)5(8)9/h3-4,6-7H,1-2H2,(H,8,9)/t3-,4-/m0/s1

InChI Key

BJBUEDPLEOHJGE-IMJSIDKUSA-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
L-alpha-amino acid
Pyrrolidine carboxylic acid
Pyrrolidine carboxylic acid or derivatives
Beta-hydroxy acid
Hydroxy acid
Pyrrolidine
Amino acid
Secondary alcohol
Carboxylic acid
Azacycle
Organoheterocyclic compound
Secondary amine
Secondary aliphatic amine
Monocarboxylic acid or derivatives
Organic oxide
Organonitrogen compound
Organooxygen compound
Alcohol
Organic oxygen compound
Carbonyl group
Hydrocarbon derivative
Amine
Organic nitrogen compound
Organopnictogen compound
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

3-hydroxy-L-proline (CHEBI:16889 )

Ontology

Not Available

Not Available

Not Available

Not Available

Physical Properties

State

Solid

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
Water Solubility	431 g/L	ALOGPS
logP	-3.2	ALOGPS
logP	-3.7	ChemAxon
logS	0.52	ALOGPS
pKa (Strongest Acidic)	1.61	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	12.33 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]+	126.749	31661259
DarkChem	[M-H]-	123.012	31661259
DeepCCS	[M+H]+	126.671	30932474
DeepCCS	[M-H]-	124.447	30932474
DeepCCS	[M-2H]-	160.043	30932474
DeepCCS	[M+Na]+	134.336	30932474
AllCCS	[M+H]+	129.0	32859911
AllCCS	[M+H-H2O]+	124.4	32859911
AllCCS	[M+NH4]+	133.4	32859911
AllCCS	[M+Na]+	134.6	32859911
AllCCS	[M-H]-	121.8	32859911
AllCCS	[M+Na-2H]-	123.8	32859911
AllCCS	[M+HCOO]-	126.1	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Trans-3-hydroxy-L-proline	[H][C@]1(O)CCN[C@]1([H])C(O)=O	2478.9	Standard polar	33892256
Trans-3-hydroxy-L-proline	[H][C@]1(O)CCN[C@]1([H])C(O)=O	1274.6	Standard non polar	33892256
Trans-3-hydroxy-L-proline	[H][C@]1(O)CCN[C@]1([H])C(O)=O	1502.1	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Trans-3-hydroxy-L-proline,1TMS,isomer #1	C[Si](C)(C)O[C@H]1CCN[C@@H]1C(=O)O	1408.6	Semi standard non polar	33892256
Trans-3-hydroxy-L-proline,1TMS,isomer #2	C[Si](C)(C)OC(=O)[C@H]1NCC[C@@H]1O	1346.0	Semi standard non polar	33892256
Trans-3-hydroxy-L-proline,1TMS,isomer #3	C[Si](C)(C)N1CC[C@H](O)[C@H]1C(=O)O	1414.9	Semi standard non polar	33892256
Trans-3-hydroxy-L-proline,2TMS,isomer #1	C[Si](C)(C)OC(=O)[C@H]1NCC[C@@H]1O[Si](C)(C)C	1444.3	Semi standard non polar	33892256
Trans-3-hydroxy-L-proline,2TMS,isomer #2	C[Si](C)(C)O[C@H]1CCN([Si](C)(C)C)[C@@H]1C(=O)O	1466.8	Semi standard non polar	33892256
Trans-3-hydroxy-L-proline,2TMS,isomer #3	C[Si](C)(C)OC(=O)[C@@H]1[C@@H](O)CCN1[Si](C)(C)C	1421.3	Semi standard non polar	33892256
Trans-3-hydroxy-L-proline,3TMS,isomer #1	C[Si](C)(C)OC(=O)[C@@H]1[C@@H](O[Si](C)(C)C)CCN1[Si](C)(C)C	1503.2	Semi standard non polar	33892256
Trans-3-hydroxy-L-proline,3TMS,isomer #1	C[Si](C)(C)OC(=O)[C@@H]1[C@@H](O[Si](C)(C)C)CCN1[Si](C)(C)C	1566.1	Standard non polar	33892256
Trans-3-hydroxy-L-proline,3TMS,isomer #1	C[Si](C)(C)OC(=O)[C@@H]1[C@@H](O[Si](C)(C)C)CCN1[Si](C)(C)C	1653.9	Standard polar	33892256
Trans-3-hydroxy-L-proline,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)O[C@H]1CCN[C@@H]1C(=O)O	1671.2	Semi standard non polar	33892256
Trans-3-hydroxy-L-proline,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC(=O)[C@H]1NCC[C@@H]1O	1588.8	Semi standard non polar	33892256
Trans-3-hydroxy-L-proline,1TBDMS,isomer #3	CC(C)(C)[Si](C)(C)N1CC[C@H](O)[C@H]1C(=O)O	1691.3	Semi standard non polar	33892256
Trans-3-hydroxy-L-proline,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)[C@H]1NCC[C@@H]1O[Si](C)(C)C(C)(C)C	1898.5	Semi standard non polar	33892256
Trans-3-hydroxy-L-proline,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)O[C@H]1CCN([Si](C)(C)C(C)(C)C)[C@@H]1C(=O)O	1939.3	Semi standard non polar	33892256
Trans-3-hydroxy-L-proline,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC(=O)[C@@H]1[C@@H](O)CCN1[Si](C)(C)C(C)(C)C	1912.2	Semi standard non polar	33892256
Trans-3-hydroxy-L-proline,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)[C@@H]1[C@@H](O[Si](C)(C)C(C)(C)C)CCN1[Si](C)(C)C(C)(C)C	2181.5	Semi standard non polar	33892256
Trans-3-hydroxy-L-proline,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)[C@@H]1[C@@H](O[Si](C)(C)C(C)(C)C)CCN1[Si](C)(C)C(C)(C)C	2192.3	Standard non polar	33892256
Trans-3-hydroxy-L-proline,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)[C@@H]1[C@@H](O[Si](C)(C)C(C)(C)C)CCN1[Si](C)(C)C(C)(C)C	2076.7	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental GC-MS	GC-MS Spectrum - Trans-3-hydroxy-L-proline GC-MS (2 TMS)	splash10-0a4i-1900000000-43167f7b02d5c91f7431	2014-06-16	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - Trans-3-hydroxy-L-proline GC-MS (3 TMS)	splash10-001i-2690000000-31769ffb5511f9fd00bf	2014-06-16	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - Trans-3-hydroxy-L-proline GC-MS (Non-derivatized)	splash10-0a4i-1900000000-43167f7b02d5c91f7431	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - Trans-3-hydroxy-L-proline GC-MS (Non-derivatized)	splash10-001i-2690000000-31769ffb5511f9fd00bf	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Trans-3-hydroxy-L-proline GC-MS (Non-derivatized) - 70eV, Positive	splash10-054o-9000000000-dc85246c192fc6318aa1	2017-09-20	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Trans-3-hydroxy-L-proline GC-MS (2 TMS) - 70eV, Positive	splash10-0a4i-4910000000-4fa1d4ed0b9aee3e1fd0	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Trans-3-hydroxy-L-proline GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Trans-3-hydroxy-L-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
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Trans-3-hydroxy-L-proline 10V, Positive-QTOF	splash10-03e9-2900000000-128ccf9715c5890c5404	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Trans-3-hydroxy-L-proline 20V, Positive-QTOF	splash10-03xr-9600000000-8c3c68532a2b86bfd028	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Trans-3-hydroxy-L-proline 40V, Positive-QTOF	splash10-0fr6-9000000000-d018e434f138775d4120	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Trans-3-hydroxy-L-proline 10V, Negative-QTOF	splash10-001r-7900000000-3230ec745853fb03ffc2	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Trans-3-hydroxy-L-proline 20V, Negative-QTOF	splash10-02u9-9300000000-8240d8b2c6fddad07085	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Trans-3-hydroxy-L-proline 40V, Negative-QTOF	splash10-0673-9000000000-a3fea27c28e95706d0ec	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Trans-3-hydroxy-L-proline 10V, Positive-QTOF	splash10-000i-9400000000-f8803de3984022a6de11	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Trans-3-hydroxy-L-proline 20V, Positive-QTOF	splash10-00kr-9000000000-7199742da3eaa66ad564	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Trans-3-hydroxy-L-proline 40V, Positive-QTOF	splash10-00kf-9000000000-f8bbde6aa62a6d9afa3b	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Trans-3-hydroxy-L-proline 10V, Negative-QTOF	splash10-001i-1900000000-df968a68e6f2ab76adc2	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Trans-3-hydroxy-L-proline 20V, Negative-QTOF	splash10-0006-9200000000-c73aa9b436f74ef75e9c	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Trans-3-hydroxy-L-proline 40V, Negative-QTOF	splash10-052f-9000000000-08bc65f1f17e8bcb3d04	2021-09-23	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

389475

KEGG Compound ID

C05147

BioCyc ID

CPD-664

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

440575

PDB ID

HY3

ChEBI ID

16889

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

Roux A, Xu Y, Heilier JF, Olivier MF, Ezan E, Tabet JC, Junot C: Annotation of the human adult urinary metabolome and metabolite identification using ultra high performance liquid chromatography coupled to a linear quadrupole ion trap-Orbitrap mass spectrometer. Anal Chem. 2012 Aug 7;84(15):6429-37. doi: 10.1021/ac300829f. Epub 2012 Jul 17. [PubMed:22770225 ]

Enzymes

Enzyme Details

1. 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

Reactions

Trans-3-hydroxy-L-proline → 1-pyrroline 2-carboxylate + Water	details

Showing metabocard for Trans-3-hydroxy-L-proline (HMDB0059659)

MOL for HMDB0059659 (Trans-3-hydroxy-L-proline)

3D MOL for HMDB0059659 (Trans-3-hydroxy-L-proline)

3D SDF for HMDB0059659 (Trans-3-hydroxy-L-proline)

3D-SDF for HMDB0059659 (Trans-3-hydroxy-L-proline)

PDB for HMDB0059659 (Trans-3-hydroxy-L-proline)

3D PDB for HMDB0059659 (Trans-3-hydroxy-L-proline)

SMILES for HMDB0059659 (Trans-3-hydroxy-L-proline)

INCHI for HMDB0059659 (Trans-3-hydroxy-L-proline)

Structure for HMDB0059659 (Trans-3-hydroxy-L-proline)

3D Structure for HMDB0059659 (Trans-3-hydroxy-L-proline)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra

Enzymes

Reactions