MiMeDB: Showing metabocard for (3R)-3-hydroxy-D-aspartic acid (MMDBc0054896)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-17 19:37:24 UTC

Update Date

2025-10-07 16:08:46 UTC

Metabolite ID

MMDBc0054896

Metabolite Identification

Common Name

(3R)-3-hydroxy-D-aspartic acid

Description

(3R)-3-hydroxy-D-aspartic acid is a non-proteinogenic amino acid belonging to the class of hydroxy acids. There is limited literature available on this metabolite, indicating a need for further research to understand its biological significance and potential applications.

Structure

MOL SDF PDB SMILES InChI

HEADER    PROTEIN                                 17-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUN-22         0                                  
HETATM    1  C   UNK     0       2.874   0.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.207  -0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.206   0.770   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       2.874   2.310   0.000  0.00  0.00           N+0
HETATM    6  O   UNK     0       1.540  -1.540   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       5.541   0.770   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       4.207  -1.540   0.000  0.00  0.00           O-1
HETATM    9  O   UNK     0      -1.127   0.000   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       0.206   2.310   0.000  0.00  0.00           O+0
HETATM   11  H   UNK     0       2.874  -0.770   0.000  0.00  0.00           H+0
HETATM   12  H   UNK     0       1.540   1.540   0.000  0.00  0.00           H+0
CONECT    1    2    3    5   11                                             
CONECT    2    1    4    6   12                                             
CONECT    3    1    7    8                                                  
CONECT    4    2    9   10                                                  
CONECT    5    1                                                            
CONECT    6    2                                                            
CONECT    7    3                                                            
CONECT    8    3                                                            
CONECT    9    4                                                            
CONECT   10    4                                                            
CONECT   11    1                                                            
CONECT   12    2                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   22    0
END

Synonyms

Value	Source
(3R)-3-Hydroxy-D-aspartate	ChEBI
Threo-3-hydroxy-D-aspartate	ChEBI
Threo-beta-hydroxy-D-aspartate	ChEBI
(3R)-3-Hydroxy-D-aspartic acid	Generator
Threo-3-hydroxy-D-aspartic acid	Generator
Threo-b-hydroxy-D-aspartate	Generator
Threo-b-hydroxy-D-aspartic acid	Generator
Threo-beta-hydroxy-D-aspartic acid	Generator
Threo-β-hydroxy-D-aspartate	Generator
Threo-β-hydroxy-D-aspartic acid	Generator
D-Threo-3-hydroxyaspartic acid	Generator

Molecular Formula

C₄H₆NO₅

Average Mass

148.095

Monoisotopic Mass

148.025145877

IUPAC Name

(2R,3R)-2-amino-3-carboxy-3-hydroxypropanoate

Traditional Name

(3R)-3-hydroxy-D-aspartate

CAS Registry Number

Not Available

SMILES

[H][C@](N)(C([O-])=O)[C@@]([H])(O)C(O)=O

InChI Identifier

InChI=1S/C4H7NO5/c5-1(3(7)8)2(6)4(9)10/h1-2,6H,5H2,(H,7,8)(H,9,10)/p-1/t1-,2-/m1/s1

InChI Key

YYLQUHNPNCGKJQ-JCYAYHJZSA-M

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as aspartic acid and derivatives. Aspartic acid and derivatives are compounds containing an aspartic acid or a derivative thereof resulting from reaction of aspartic acid 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

Aspartic acid and derivatives

Alternative Parents

Substituents

Aspartic acid or derivatives
Alpha-amino acid
D-alpha-amino acid
Beta-hydroxy acid
Short-chain hydroxy acid
Dicarboxylic acid or derivatives
Hydroxy acid
Fatty acid
Carboxylic acid salt
Secondary alcohol
Amino acid
Carboxylic acid
Organic nitrogen compound
Primary amine
Organooxygen compound
Organonitrogen compound
Primary aliphatic amine
Organic oxide
Organopnictogen compound
Alcohol
Carbonyl group
Organic oxygen compound
Amine
Organic salt
Hydrocarbon derivative
Organic anion
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

dicarboxylic acid anion (CHEBI:60898 )
D-alpha-amino acid anion (CHEBI:60898 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-4.4	ChemAxon
pKa (Strongest Acidic)	2.57	ChemAxon
pKa (Strongest Basic)	9.08	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	123.68 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	38.71 m³·mol⁻¹	ChemAxon
Polarizability	11.72 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Not Available

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	566.3
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-24	398.2
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (void)	2025-10-24	44.5
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-24	247.5
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (void)	2025-10-24	316.7
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (void)	2025-10-24	394.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-24	586.2
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	880.5
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-24	1045.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	236.8
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	454.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-24	253.1
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-24	37.1
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	481.6
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	756.8
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-24	118.2
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-24	370.6
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-24	778.0
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-24	646.2

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	(3R)-3-hydroxy-D-aspartic acid_TMS_1	C[Si](C)(C)O[C@@H](C(=O)O)[C@@H](N)C(=O)[O-]	standard non polar	2025-10-24	2055.71
Gas Chromatography	(3R)-3-hydroxy-D-aspartic acid_TMS_2	C[Si](C)(C)OC(=O)[C@H](O)[C@@H](N)C(=O)[O-]	standard non polar	2025-10-24	1904.7
Gas Chromatography	(3R)-3-hydroxy-D-aspartic acid_TMS_3	C[Si](C)(C)N[C@@H](C(=O)[O-])[C@@H](O)C(=O)O	standard non polar	2025-10-24	1899.47
Gas Chromatography	(3R)-3-hydroxy-D-aspartic acid_TMS_4	C[Si](C)(C)OC(=O)[C@H](O[Si](C)(C)C)[C@@H](N)C(=O)[O-]	standard non polar	2025-10-24	1384.31
Gas Chromatography	(3R)-3-hydroxy-D-aspartic acid_TMS_5	C[Si](C)(C)N[C@@H](C(=O)[O-])[C@@H](O[Si](C)(C)C)C(=O)O	standard non polar	2025-10-24	2070.92
Gas Chromatography	(3R)-3-hydroxy-D-aspartic acid_TMS_6	C[Si](C)(C)N[C@@H](C(=O)[O-])[C@@H](O)C(=O)O[Si](C)(C)C	standard non polar	2025-10-24	1579.25
Gas Chromatography	(3R)-3-hydroxy-D-aspartic acid_TMS_7	C[Si](C)(C)N([C@@H](C(=O)[O-])[C@@H](O)C(=O)O)[Si](C)(C)C	standard non polar	2025-10-24	1599.06
Gas Chromatography	(3R)-3-hydroxy-D-aspartic acid_TMS_8	C[Si](C)(C)N[C@@H](C(=O)[O-])[C@@H](O[Si](C)(C)C)C(=O)O[Si](C)(C)C	standard non polar	2025-10-24	2541.14
Gas Chromatography	(3R)-3-hydroxy-D-aspartic acid_TMS_9	C[Si](C)(C)O[C@@H](C(=O)O)[C@H](C(=O)[O-])N([Si](C)(C)C)[Si](C)(C)C	standard non polar	2025-10-24	1414.53
Gas Chromatography	(3R)-3-hydroxy-D-aspartic acid_TMS_10	C[Si](C)(C)OC(=O)[C@H](O)[C@H](C(=O)[O-])N([Si](C)(C)C)[Si](C)(C)C	standard non polar	2025-10-24	1945.34
Gas Chromatography	(3R)-3-hydroxy-D-aspartic acid_TMS_11	C[Si](C)(C)OC(=O)[C@H](O[Si](C)(C)C)[C@H](C(=O)[O-])N([Si](C)(C)C)[Si](C)(C)C	standard non polar	2025-10-24	1660.23
Gas Chromatography	(3R)-3-hydroxy-D-aspartic acid_TMS_1	C[Si](C)(C)O[C@@H](C(=O)O)[C@@H](N)C(=O)[O-]	standard polar	2025-10-24	1613.48
Gas Chromatography	(3R)-3-hydroxy-D-aspartic acid_TMS_2	C[Si](C)(C)OC(=O)[C@H](O)[C@@H](N)C(=O)[O-]	standard polar	2025-10-24	2206.42
Gas Chromatography	(3R)-3-hydroxy-D-aspartic acid_TMS_3	C[Si](C)(C)N[C@@H](C(=O)[O-])[C@@H](O)C(=O)O	standard polar	2025-10-24	1981.07
Gas Chromatography	(3R)-3-hydroxy-D-aspartic acid_TMS_4	C[Si](C)(C)OC(=O)[C@H](O[Si](C)(C)C)[C@@H](N)C(=O)[O-]	standard polar	2025-10-24	1873.25
Gas Chromatography	(3R)-3-hydroxy-D-aspartic acid_TMS_5	C[Si](C)(C)N[C@@H](C(=O)[O-])[C@@H](O[Si](C)(C)C)C(=O)O	standard polar	2025-10-24	2269.62
Gas Chromatography	(3R)-3-hydroxy-D-aspartic acid_TMS_6	C[Si](C)(C)N[C@@H](C(=O)[O-])[C@@H](O)C(=O)O[Si](C)(C)C	standard polar	2025-10-24	1969.1
Gas Chromatography	(3R)-3-hydroxy-D-aspartic acid_TMS_7	C[Si](C)(C)N([C@@H](C(=O)[O-])[C@@H](O)C(=O)O)[Si](C)(C)C	standard polar	2025-10-24	2030.37
Gas Chromatography	(3R)-3-hydroxy-D-aspartic acid_TMS_8	C[Si](C)(C)N[C@@H](C(=O)[O-])[C@@H](O[Si](C)(C)C)C(=O)O[Si](C)(C)C	standard polar	2025-10-24	2606.77
Gas Chromatography	(3R)-3-hydroxy-D-aspartic acid_TMS_9	C[Si](C)(C)O[C@@H](C(=O)O)[C@H](C(=O)[O-])N([Si](C)(C)C)[Si](C)(C)C	standard polar	2025-10-24	2968.52
Gas Chromatography	(3R)-3-hydroxy-D-aspartic acid_TMS_10	C[Si](C)(C)OC(=O)[C@H](O)[C@H](C(=O)[O-])N([Si](C)(C)C)[Si](C)(C)C	standard polar	2025-10-24	2368.51
Gas Chromatography	(3R)-3-hydroxy-D-aspartic acid_TMS_11	C[Si](C)(C)OC(=O)[C@H](O[Si](C)(C)C)[C@H](C(=O)[O-])N([Si](C)(C)C)[Si](C)(C)C	standard polar	2025-10-24	2073.65

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	Microbial Links
Bacteria/Eubacteria	Proteobacteria	2
Bacteria	Proteobacteria	1

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

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

26332033

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

40468139

PDB ID

Not Available

ChEBI ID

60898

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 (3R)-3-hydroxy-D-aspartic acid (MMDBc0054896)

MOL for #<Metabolite:0x00005643200e72e8>

3D MOL for #<Metabolite:0x00005643200e72e8>

3D SDF for #<Metabolite:0x00005643200e72e8>

3D-SDF for #<Metabolite:0x00005643200e72e8>

PDB for #<Metabolite:0x00005643200e72e8>

3D PDB for #<Metabolite:0x00005643200e72e8>

SMILES for #<Metabolite:0x00005643200e72e8>

INCHI for #<Metabolite:0x00005643200e72e8>

Structure for #<Metabolite:0x00005643200e72e8>

3D Structure for #<Metabolite:0x00005643200e72e8>