MiMeDB: Showing metabocard for 5-hydroxyectoine (MMDBc0054281)

Xenobiotic

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-05 23:04:21 UTC

Update Date

2025-10-07 16:08:27 UTC

Metabolite ID

MMDBc0054281

Metabolite Identification

Common Name

5-hydroxyectoine

Description

5-hydroxyectoine is a compatible solute belonging to the class of hydroxyectoines, which are derived from the naturally occurring osmoprotectant ectoine. Chemically, 5-hydroxyectoine is characterized by the presence of a hydroxyl group at the 5-position of the ectoine structure, which consists of a pyrrolidine ring and a carboxylate group. This modification enhances its solubility and stability under osmotic stress conditions. In terms of biological pathways, 5-hydroxyectoine is involved in the catabolism of compatible solutes, as indicated by the identification of a gene cluster that facilitates the degradation of both ectoine and 5-hydroxyectoine (PMID:39699277 ). This pathway plays a crucial role in microbial adaptation to osmotic stress, allowing organisms to maintain cellular integrity and function in extreme environments. The structural modifications of 5-hydroxyectoine compared to ectoine suggest potential differences in their biological roles and mechanisms of action within the cellular milieu.

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 05031422482D          

 13 13  0  0  1  0            999 V2000
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    1.6500    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    1.6500    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  4  1  0  0  0  0
  5  6  1  6  0  0  0
  7  2  1  0  0  0  0
  7  3  2  0  0  0  0
  8  3  1  0  0  0  0
  8  5  1  0  0  0  0
  4  9  1  1  0  0  0
 10  6  2  0  0  0  0
 11  6  1  0  0  0  0
  4 12  1  6  0  0  0
  5 13  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0054281

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]1(O)CN=C(C)N[C@]1([H])C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C6H10N2O3/c1-3-7-2-4(9)5(8-3)6(10)11/h4-5,9H,2H2,1H3,(H,7,8)(H,10,11)/t4-,5-/m0/s1

> <INCHI_KEY>
KIIBBJKLKFTNQO-WHFBIAKZSA-N

> <FORMULA>
C6H10N2O3

> <MOLECULAR_WEIGHT>
158.1552

> <EXACT_MASS>
158.069142196

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
14.781213093572264

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4S,5S)-5-hydroxy-2-methyl-3,4,5,6-tetrahydropyrimidine-4-carboxylic acid

> <ALOGPS_LOGP>
-1.13

> <JCHEM_LOGP>
-3.216322549786173

> <ALOGPS_LOGS>
-0.95

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.970593260107552

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.6075517555611194

> <JCHEM_PKA_STRONGEST_BASIC>
9.247754481337447

> <JCHEM_POLAR_SURFACE_AREA>
81.92

> <JCHEM_REFRACTIVITY>
36.1398

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.77e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-hydroxyectoine

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 03-MAY-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-MAY-14         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM    8  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM    9  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   12  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   13  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    3                                                            
CONECT    2    4    7                                                       
CONECT    3    1    7    8                                                  
CONECT    4    2    5    9   12                                             
CONECT    5    4    6    8   13                                             
CONECT    6    5   10   11                                                  
CONECT    7    2    3                                                       
CONECT    8    3    5                                                       
CONECT    9    4                                                            
CONECT   10    6                                                            
CONECT   11    6                                                            
CONECT   12    4                                                            
CONECT   13    5                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   26    0
END

Synonyms

Value	Source
(4S,5S)-2-Methyl-4-carboxy-5-hydroxy-3,4,5,6-tetrahydropyrimidine	ChEBI
(4S,5S)-5-HYDROXY-2-methyl-1,4,5,6-tetrahydropyrimidine-4-carboxylIC ACID	ChEBI
(S,S)-2-Methyl-5-hydroxy-1,4,5,6-tetrahydropyrimidine-4-carboxylic acid	ChEBI
beta-Hydroxyectoine	ChEBI
Hydroxyectoine	ChEBI
(4S,5S)-5-HYDROXY-2-methyl-1,4,5,6-tetrahydropyrimidine-4-carboxylate	Generator
(S,S)-2-Methyl-5-hydroxy-1,4,5,6-tetrahydropyrimidine-4-carboxylate	Generator
b-Hydroxyectoine	Generator
Β-hydroxyectoine	Generator
5-Hydroxyectoine	MeSH

Molecular Formula

C₆H₁₀N₂O₃

Average Mass

158.1552

Monoisotopic Mass

158.069142196

IUPAC Name

(4S,5S)-5-hydroxy-2-methyl-3,4,5,6-tetrahydropyrimidine-4-carboxylic acid

Traditional Name

5-hydroxyectoine

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C6H10N2O3/c1-3-7-2-4(9)5(8-3)6(10)11/h4-5,9H,2H2,1H3,(H,7,8)(H,10,11)/t4-,5-/m0/s1

InChI Key

KIIBBJKLKFTNQO-WHFBIAKZSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

L-alpha-amino acids

Alternative Parents

Substituents

L-alpha-amino acid
Hydropyrimidine carboxylic acid derivative
Beta-hydroxy acid
Hydropyrimidine
1,4,5,6-tetrahydropyrimidine
Hydroxy acid
Imidolactam
Secondary alcohol
Amidine
Carboxylic acid amidine
Carboxylic acid
Monocarboxylic acid or derivatives
Azacycle
Carboximidamide
Propargyl-type 1,3-dipolar organic compound
Organic 1,3-dipolar compound
Organoheterocyclic compound
Organic oxide
Hydrocarbon derivative
Organic nitrogen compound
Organonitrogen compound
Organooxygen compound
Carbonyl group
Alcohol
Organic oxygen compound
Organopnictogen compound
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

iminium betaine (CHEBI:85413 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	17.7 g/L	ALOGPS
logP	-1.1	ALOGPS
logP	-3.2	ChemAxon
logS	-0.95	ALOGPS
pKa (Strongest Acidic)	2.61	ChemAxon
pKa (Strongest Basic)	9.25	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	81.92 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	36.14 m³·mol⁻¹	ChemAxon
Polarizability	14.78 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 (TMS_1_1) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-052f-0900000000-abd891a4570682f765b3	2019-02-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03dl-1900000000-abe7f8ff0e73a01a76e1	2019-02-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0006-9000000000-961e39aabd5018ec55f9	2019-02-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0bt9-1900000000-d5dd239ec5b802cb7432	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-03di-5900000000-ae9f9da2de49174e2112	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0ukc-9000000000-7f02ba344ab67a14b5d7	2019-02-23	View Spectrum
MS	Mass Spectrum (Electron Ionization)	Not Available	2022-08-06	View Spectrum

Chromatographic Retention Times and Retention Indices

Retention Times

Chromatography Type	Technique	Column	Deposition Date	Retention Time (s)
Liquid Chromatography	HILIC	Waters Acquity UPLC-BEH Amide column (eluted)	2025-10-24	426.6
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-24	283.6
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (void)	2025-10-24	56.3
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-24	238.3
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-24	275.5
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (void)	2025-10-24	311.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	686.6
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	595.1
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-24	785.5
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	163.0
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	316.8
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	177.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	51.0
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	250.3
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	589.0
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-24	61.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	204.3
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-24	813.8
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-24	598.7

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	5-hydroxyectoine_TMS_1	CC1=NC[C@H](O[Si](C)(C)C)[C@@H](C(=O)O)N1	standard non polar	2025-10-24	1867.24
Gas Chromatography	5-hydroxyectoine_TMS_2	CC1=NC[C@H](O)[C@@H](C(=O)O[Si](C)(C)C)N1	standard non polar	2025-10-24	2267.56
Gas Chromatography	5-hydroxyectoine_TMS_3	CC1=NC[C@H](O)[C@@H](C(=O)O)N1[Si](C)(C)C	standard non polar	2025-10-24	1433.51
Gas Chromatography	5-hydroxyectoine_TMS_4	CC1=NC[C@H](O[Si](C)(C)C)[C@@H](C(=O)O[Si](C)(C)C)N1	standard non polar	2025-10-24	1808.92
Gas Chromatography	5-hydroxyectoine_TMS_5	CC1=NC[C@H](O[Si](C)(C)C)[C@@H](C(=O)O)N1[Si](C)(C)C	standard non polar	2025-10-24	2425.37
Gas Chromatography	5-hydroxyectoine_TMS_6	CC1=NC[C@H](O)[C@@H](C(=O)O[Si](C)(C)C)N1[Si](C)(C)C	standard non polar	2025-10-24	1867.14
Gas Chromatography	5-hydroxyectoine_TMS_7	CC1=NC[C@H](O[Si](C)(C)C)[C@@H](C(=O)O[Si](C)(C)C)N1[Si](C)(C)C	standard non polar	2025-10-24	2367.05
Gas Chromatography	5-hydroxyectoine_TMS_1	CC1=NC[C@H](O[Si](C)(C)C)[C@@H](C(=O)O)N1	standard polar	2025-10-24	2669.89
Gas Chromatography	5-hydroxyectoine_TMS_2	CC1=NC[C@H](O)[C@@H](C(=O)O[Si](C)(C)C)N1	standard polar	2025-10-24	2144.52
Gas Chromatography	5-hydroxyectoine_TMS_3	CC1=NC[C@H](O)[C@@H](C(=O)O)N1[Si](C)(C)C	standard polar	2025-10-24	1880.44
Gas Chromatography	5-hydroxyectoine_TMS_4	CC1=NC[C@H](O[Si](C)(C)C)[C@@H](C(=O)O[Si](C)(C)C)N1	standard polar	2025-10-24	2019.89
Gas Chromatography	5-hydroxyectoine_TMS_5	CC1=NC[C@H](O[Si](C)(C)C)[C@@H](C(=O)O)N1[Si](C)(C)C	standard polar	2025-10-24	1947.57
Gas Chromatography	5-hydroxyectoine_TMS_6	CC1=NC[C@H](O)[C@@H](C(=O)O[Si](C)(C)C)N1[Si](C)(C)C	standard polar	2025-10-24	2118.93
Gas Chromatography	5-hydroxyectoine_TMS_7	CC1=NC[C@H](O[Si](C)(C)C)[C@@H](C(=O)O[Si](C)(C)C)N1[Si](C)(C)C	standard polar	2025-10-24	1129.82

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

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

Human Pathways

Pathways

Name	SMPDB/PathBank

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

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
Bacteria/Eubacteria	Proteobacteria	6
Bacteria/Eubacteria	Actinobacteria	4	Human
Bacteria	Firmicutes	1

Exposure Sources

Other Exposures

Source Type	Data Source	Reference
Cosmetics	U.S. Environmental Protection Agency	CompTox
Domestics	U.S. Environmental Protection Agency	CompTox
Cosmetics	U.S. Environmental Protection Agency	CompTox

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

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

C16432

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

12011795

PDB ID

Not Available

ChEBI ID

49432

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for 5-hydroxyectoine (MMDBc0054281)

MOL for #<Metabolite:0x00005643233f2e80>

3D MOL for #<Metabolite:0x00005643233f2e80>

3D SDF for #<Metabolite:0x00005643233f2e80>

3D-SDF for #<Metabolite:0x00005643233f2e80>

PDB for #<Metabolite:0x00005643233f2e80>

3D PDB for #<Metabolite:0x00005643233f2e80>

SMILES for #<Metabolite:0x00005643233f2e80>

INCHI for #<Metabolite:0x00005643233f2e80>

Structure for #<Metabolite:0x00005643233f2e80>

3D Structure for #<Metabolite:0x00005643233f2e80>