MiMeDB: Showing metabocard for D-Valine (MMDBc0000289)

Microbial

Xenobiotic

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2020-10-28 00:08:45 UTC

Update Date

2025-10-07 16:04:13 UTC

Metabolite ID

MMDBc0000289

Metabolite Identification

Common Name

D-Valine

Description

D-Valine is a non-proteinogenic amino acid belonging to the class of branched-chain amino acids. Its chemical structure features a branched aliphatic side chain, which distinguishes it from its L-enantiomer. D-Valine participates in various biochemical pathways, including the metabolic detoxification processes mediated by d-amino acid oxidase (DAO), which converts non-toxic D-valine into cytotoxic products, thereby allowing for selective enrichment of genetically modified plants (PMID:38974862 ). Additionally, D-Valine has been implicated in the regulation of interfacial properties in aqueous zinc ion batteries, where its anionic forms contribute to efficient proton transport and electric field dynamics (PMID:40202425 ). Furthermore, D-Valine has been shown to enhance levels of sphingomyelins and other metabolites in specific supplementation studies (PMID:39271063 ). It also serves as a substrate for the synthesis of thiohydantoins, which exhibit significant inhibitory effects on ureolytic activity in fungal lysates (PMID:40714478 ). The versatility of D-Valine in both synthetic and biological contexts underscores its importance in various chemical and biological systems.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
(2R)-2-Amino-3-methylbutanoic acid	ChEBI
(R)-2-Amino-3-methylbutyric acid	ChEBI
(R)-Valine	ChEBI
D-Valin	ChEBI
DVA	ChEBI
(2R)-2-Amino-3-methylbutanoate	Generator
(R)-2-Amino-3-methylbutyrate	Generator

Molecular Formula

C₅H₁₁NO₂

Average Mass

117.1463

Monoisotopic Mass

117.078978601

IUPAC Name

(2R)-2-amino-3-methylbutanoic acid

Traditional Name

D-valine

CAS Registry Number

640-68-6

SMILES

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

InChI Identifier

InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m1/s1

InChI Key

KZSNJWFQEVHDMF-SCSAIBSYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as valine and derivatives. Valine and derivatives are compounds containing valine or a derivative thereof resulting from reaction of valine 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

Valine and derivatives

Alternative Parents

Substituents

Valine or derivatives
Alpha-amino acid
D-alpha-amino acid
Branched fatty acid
Methyl-branched fatty acid
Fatty acid
Fatty acyl
Amino acid
Monocarboxylic acid or derivatives
Carboxylic acid
Organic oxide
Organopnictogen compound
Primary amine
Organooxygen compound
Organonitrogen compound
Primary aliphatic amine
Carbonyl group
Organic oxygen compound
Amine
Organic nitrogen compound
Hydrocarbon derivative
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

D-alpha-amino acid (CHEBI:27477 )
valine (CHEBI:27477 )
Other amino acids (C06417 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	214 g/L	ALOGPS
logP	-2.3	ALOGPS
logP	-2	ChemAxon
logS	0.26	ALOGPS
pKa (Strongest Acidic)	2.72	ChemAxon
pKa (Strongest Basic)	9.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	63.32 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	29.49 m³·mol⁻¹	ChemAxon
Polarizability	12.19 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

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-00dl-9000000000-602d1e01bc7567493e4c	2016-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-00xr-9500000000-bb54662a5fd1dd142d90	2016-08-02	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-00di-9000000000-1f7d9c10db4226a383c1	2016-08-02	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-05fu-9000000000-f6d7e45bb3f3436e5eb7	2016-08-02	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-014i-2900000000-f5c404ed60b91c5f9cb9	2016-08-03	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-014i-5900000000-b6ba2bbf6fc32d3451e7	2016-08-03	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-00di-9000000000-0374f01d56dca105471a	2016-08-03	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-23	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)	2025-10-23	447.5
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-23	340.4
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (void)	2025-10-23	66.5
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-23	241.7
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (void)	2025-10-23	300.3
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (void)	2025-10-23	342.1
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-23	607.6
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-23	561.8
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-23	651.1
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	192.8
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-23	417.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-23	201.8
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	60.2
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	299.8
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	521.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-23	50.9
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-23	261.6
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (void)	2025-10-23	697.5
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-23	626.0

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	D-Valine_TMS_1	CC(C)[C@@H](N)C(=O)O[Si](C)(C)C	standard non polar	2025-10-23	1951.54
Gas Chromatography	D-Valine_TMS_2	CC(C)[C@@H](N[Si](C)(C)C)C(=O)O	standard non polar	2025-10-23	2066.59
Gas Chromatography	D-Valine_TMS_3	CC(C)[C@@H](N[Si](C)(C)C)C(=O)O[Si](C)(C)C	standard non polar	2025-10-23	2408.56
Gas Chromatography	D-Valine_TMS_4	CC(C)[C@H](C(=O)O)N([Si](C)(C)C)[Si](C)(C)C	standard non polar	2025-10-23	2115.87
Gas Chromatography	D-Valine_TMS_5	CC(C)[C@H](C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C	standard non polar	2025-10-23	2114.27
Gas Chromatography	D-Valine_TMS_1	CC(C)[C@@H](N)C(=O)O[Si](C)(C)C	standard polar	2025-10-23	2090.56
Gas Chromatography	D-Valine_TMS_2	CC(C)[C@@H](N[Si](C)(C)C)C(=O)O	standard polar	2025-10-23	2048.21
Gas Chromatography	D-Valine_TMS_3	CC(C)[C@@H](N[Si](C)(C)C)C(=O)O[Si](C)(C)C	standard polar	2025-10-23	2342.4
Gas Chromatography	D-Valine_TMS_4	CC(C)[C@H](C(=O)O)N([Si](C)(C)C)[Si](C)(C)C	standard polar	2025-10-23	2263.84
Gas Chromatography	D-Valine_TMS_5	CC(C)[C@H](C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C	standard polar	2025-10-23	2040.6

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
MMDBr0026121	D-Valine	N-Acetyl-D-valine	D-amino-acid N-acetyltransferase HPA3	Acetylation	RHEA	34755880
MMDBr0026134	L-Valine	D-Valine	Broad substrate specificity amino-acid racemase	Racemization	RHEA	34755880
MMDBr0039023	L-Valine	D-Valine	Broad specificity amino-acid racemase	Racemization	RHEA	34755880

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
Eukaryota/Fungi	Ascomycota	1	Human feces; Human saliva	Unknown

Exposure Sources

Other Exposures

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

C06417

BioCyc ID

CPD-3642

BiGG ID

Not Available

Wikipedia Link

Valine

METLIN ID

Not Available

PubChem Compound

71563

PDB ID

Not Available

ChEBI ID

27477

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]

Showing metabocard for D-Valine (MMDBc0000289)

MOL for #<Metabolite:0x00007fade0772730>

3D MOL for #<Metabolite:0x00007fade0772730>

3D SDF for #<Metabolite:0x00007fade0772730>

3D-SDF for #<Metabolite:0x00007fade0772730>

PDB for #<Metabolite:0x00007fade0772730>

3D PDB for #<Metabolite:0x00007fade0772730>

SMILES for #<Metabolite:0x00007fade0772730>

INCHI for #<Metabolite:0x00007fade0772730>

Structure for #<Metabolite:0x00007fade0772730>

3D Structure for #<Metabolite:0x00007fade0772730>