MiMeDB: Showing metabocard for cis-4-Hydroxy-D-proline (MMDBc0049953)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-04-29 22:46:59 UTC

Update Date

2024-04-30 20:41:52 UTC

Metabolite ID

MMDBc0049953

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

Synonyms

Not Available

Molecular Formula

C₅H₉NO₃

Average Mass

131.1299

Monoisotopic Mass

131.058243159

IUPAC Name

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

Traditional Name

cis-4-hydroxy-D-proline

CAS Registry Number

Not Available

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 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted 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

Spectra

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

Not Available

Biospecimen Locations

Feces

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

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0008342	4-Hydroxyproline	cis-4-Hydroxy-D-proline	Not Available		VMH	30371894
MMDBr0008343	cis-4-Hydroxy-D-proline	1-Pyrroline-4-hydroxy-2-carboxylate	Not Available		VMH	30371894

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
Bacteria	Proteobacteria	77	Human feces; Human sputum; Human ; Sheep ; Pig	Metabolic reconstruction
Bacteria	Actinobacteria	5	Human feces	Metabolic reconstruction
Bacteria	Firmicutes	20	Human ; Human feces	Metabolic reconstruction
Bacteria	Bacteroidetes	4	Human feces	Metabolic reconstruction
Bacteria	Planctomycetes	2	Human feces	Metabolic reconstruction

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 Feces	Detected but not Quantified									HMDB

External Links

HMDB ID

HMDB0060460

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

References

Synthesis Reference

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 ]

Showing metabocard for cis-4-Hydroxy-D-proline (MMDBc0049953)

MOL for #<Metabolite:0x00007fecae6a8770>

3D MOL for #<Metabolite:0x00007fecae6a8770>

3D SDF for #<Metabolite:0x00007fecae6a8770>

3D-SDF for #<Metabolite:0x00007fecae6a8770>

PDB for #<Metabolite:0x00007fecae6a8770>

3D PDB for #<Metabolite:0x00007fecae6a8770>

SMILES for #<Metabolite:0x00007fecae6a8770>

INCHI for #<Metabolite:0x00007fecae6a8770>

Structure for #<Metabolite:0x00007fecae6a8770>

3D Structure for #<Metabolite:0x00007fecae6a8770>