MiMeDB: Showing metabocard for (2R,4S)-2,4-diaminopentanoic acid (MMDBc0054042)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-05 22:47:55 UTC

Update Date

2025-10-07 16:08:20 UTC

Metabolite ID

MMDBc0054042

Metabolite Identification

Common Name

(2R,4S)-2,4-diaminopentanoic acid

Description

(2R,4S)-2,4-diaminopentanoic acid is a member of the amino acid class, specifically a diamino acid. Its chemical structure features a pentane backbone with two amino groups located at the 2nd and 4th carbon positions, which contributes to its unique properties and reactivity. This compound is synthesized through the enzymatic action of ornithine 4,5-aminomutase, an enzyme that utilizes adenosylcobalamin (AdoCbl) and pyridoxal L-phosphate (PLP) as cofactors to facilitate the rearrangement of D-ornithine into (2R,4S)-2,4-diaminopentanoic acid (PMID:18948256 ). Additionally, D-ornithine aminomutase from Clostridium sticklandii is known to catalyze the reversible transformation of D-ornithine to this compound, highlighting its role in amino acid metabolism (PMID:11577113 ). The presence of this metabolite in various biochemical pathways underscores its potential significance in microbial metabolism and amino acid synthesis, although its specific biological roles require further investigation.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
(2R,4S)-2,4-Diaminopentanoate	ChEBI
D-Threo-2,4-diaminopentanoate	ChEBI
2,4-Diaminopentanoate	Kegg
D-Threo-2,4-diaminopentanoic acid	Generator
2,4-Diaminopentanoic acid	Generator
(2R,4S)-2,4-Diaminopentanoic acid	Generator

Molecular Formula

C₅H₁₂N₂O₂

Average Mass

132.163

Monoisotopic Mass

132.089877634

IUPAC Name

(2R,4S)-2,4-diaminopentanoic acid

Traditional Name

D-threo-2,4-diaminopentanoate

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C5H12N2O2/c1-3(6)2-4(7)5(8)9/h3-4H,2,6-7H2,1H3,(H,8,9)/t3-,4+/m0/s1

InChI Key

PCEJMSIIDXUDSN-IUYQGCFVSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as d-alpha-amino acids. These are alpha amino acids which have the D-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

D-alpha-amino acids

Alternative Parents

Substituents

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

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

2,4-diaminopentanoic acid (CHEBI:4280 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	213 g/L	ALOGPS
logP	-3.7	ALOGPS
logP	-3.6	ChemAxon
logS	0.21	ALOGPS
pKa (Strongest Acidic)	2.64	ChemAxon
pKa (Strongest Basic)	10.45	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	89.34 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	32.98 m³·mol⁻¹	ChemAxon
Polarizability	13.67 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 (TMS_4_1) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-015i-7900000000-12f0e3130ce2aa90ac89	2019-02-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-00dr-9000000000-c2b7bbeee8ac8b72ac38	2019-02-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-00di-9000000000-17dad19e282e4d0c56bd	2019-02-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-001i-1900000000-eb058d5405e79ae1a026	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-01x0-5900000000-1ed7652204ddf9ee9f8b	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-00di-9000000000-22cfa596e4abcce9c4ad	2019-02-23	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-21	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	532.2
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-24	449.9
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (void)	2025-10-24	37.3
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-24	221.9
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-24	289.8
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (void)	2025-10-24	303.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-24	371.7
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	917.8
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-24	771.9
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	179.9
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	689.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	186.8
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	35.9
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	443.1
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	803.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	72.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-24	311.3
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-24	565.3
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-24	559.9

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	(2R,4S)-2,4-diaminopentanoic acid_TMS_1	C[C@H](N)C[C@@H](N)C(=O)O[Si](C)(C)C	standard non polar	2025-10-24	2173.76
Gas Chromatography	(2R,4S)-2,4-diaminopentanoic acid_TMS_2	C[C@@H](C[C@@H](N)C(=O)O)N[Si](C)(C)C	standard non polar	2025-10-24	1922.06
Gas Chromatography	(2R,4S)-2,4-diaminopentanoic acid_TMS_3	C[C@H](N)C[C@@H](N[Si](C)(C)C)C(=O)O	standard non polar	2025-10-24	1929.84
Gas Chromatography	(2R,4S)-2,4-diaminopentanoic acid_TMS_4	C[C@@H](C[C@@H](N)C(=O)O[Si](C)(C)C)N[Si](C)(C)C	standard non polar	2025-10-24	1739.96
Gas Chromatography	(2R,4S)-2,4-diaminopentanoic acid_TMS_5	C[C@H](N)C[C@@H](N[Si](C)(C)C)C(=O)O[Si](C)(C)C	standard non polar	2025-10-24	1518.52
Gas Chromatography	(2R,4S)-2,4-diaminopentanoic acid_TMS_6	C[C@@H](C[C@@H](N[Si](C)(C)C)C(=O)O)N[Si](C)(C)C	standard non polar	2025-10-24	1770.26
Gas Chromatography	(2R,4S)-2,4-diaminopentanoic acid_TMS_7	C[C@@H](C[C@@H](N)C(=O)O)N([Si](C)(C)C)[Si](C)(C)C	standard non polar	2025-10-24	1850.95
Gas Chromatography	(2R,4S)-2,4-diaminopentanoic acid_TMS_8	C[C@H](N)C[C@H](C(=O)O)N([Si](C)(C)C)[Si](C)(C)C	standard non polar	2025-10-24	1932.43
Gas Chromatography	(2R,4S)-2,4-diaminopentanoic acid_TMS_9	C[C@@H](C[C@@H](N[Si](C)(C)C)C(=O)O[Si](C)(C)C)N[Si](C)(C)C	standard non polar	2025-10-24	1805.18
Gas Chromatography	(2R,4S)-2,4-diaminopentanoic acid_TMS_10	C[C@@H](C[C@@H](N)C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C	standard non polar	2025-10-24	2000.32
Gas Chromatography	(2R,4S)-2,4-diaminopentanoic acid_TMS_11	C[C@H](N)C[C@H](C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C	standard non polar	2025-10-24	1823.27
Gas Chromatography	(2R,4S)-2,4-diaminopentanoic acid_TMS_12	C[C@@H](C[C@H](C(=O)O)N([Si](C)(C)C)[Si](C)(C)C)N[Si](C)(C)C	standard non polar	2025-10-24	2269.43
Gas Chromatography	(2R,4S)-2,4-diaminopentanoic acid_TMS_13	C[C@@H](C[C@@H](N[Si](C)(C)C)C(=O)O)N([Si](C)(C)C)[Si](C)(C)C	standard non polar	2025-10-24	2116.54
Gas Chromatography	(2R,4S)-2,4-diaminopentanoic acid_TMS_14	C[C@@H](C[C@H](C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C)N[Si](C)(C)C	standard non polar	2025-10-24	2246.56
Gas Chromatography	(2R,4S)-2,4-diaminopentanoic acid_TMS_15	C[C@@H](C[C@@H](N[Si](C)(C)C)C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C	standard non polar	2025-10-24	2393.11
Gas Chromatography	(2R,4S)-2,4-diaminopentanoic acid_TMS_16	C[C@@H](C[C@H](C(=O)O)N([Si](C)(C)C)[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C	standard non polar	2025-10-24	1235.75
Gas Chromatography	(2R,4S)-2,4-diaminopentanoic acid_TMS_17	C[C@@H](C[C@H](C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C	standard non polar	2025-10-24	2222.07
Gas Chromatography	(2R,4S)-2,4-diaminopentanoic acid_TMS_1	C[C@H](N)C[C@@H](N)C(=O)O[Si](C)(C)C	standard polar	2025-10-24	1999.81
Gas Chromatography	(2R,4S)-2,4-diaminopentanoic acid_TMS_2	C[C@@H](C[C@@H](N)C(=O)O)N[Si](C)(C)C	standard polar	2025-10-24	2026.58
Gas Chromatography	(2R,4S)-2,4-diaminopentanoic acid_TMS_3	C[C@H](N)C[C@@H](N[Si](C)(C)C)C(=O)O	standard polar	2025-10-24	2019.95
Gas Chromatography	(2R,4S)-2,4-diaminopentanoic acid_TMS_4	C[C@@H](C[C@@H](N)C(=O)O[Si](C)(C)C)N[Si](C)(C)C	standard polar	2025-10-24	1733.46
Gas Chromatography	(2R,4S)-2,4-diaminopentanoic acid_TMS_5	C[C@H](N)C[C@@H](N[Si](C)(C)C)C(=O)O[Si](C)(C)C	standard polar	2025-10-24	2063.6
Gas Chromatography	(2R,4S)-2,4-diaminopentanoic acid_TMS_6	C[C@@H](C[C@@H](N[Si](C)(C)C)C(=O)O)N[Si](C)(C)C	standard polar	2025-10-24	1736.2
Gas Chromatography	(2R,4S)-2,4-diaminopentanoic acid_TMS_7	C[C@@H](C[C@@H](N)C(=O)O)N([Si](C)(C)C)[Si](C)(C)C	standard polar	2025-10-24	2558.37
Gas Chromatography	(2R,4S)-2,4-diaminopentanoic acid_TMS_8	C[C@H](N)C[C@H](C(=O)O)N([Si](C)(C)C)[Si](C)(C)C	standard polar	2025-10-24	2365.61
Gas Chromatography	(2R,4S)-2,4-diaminopentanoic acid_TMS_9	C[C@@H](C[C@@H](N[Si](C)(C)C)C(=O)O[Si](C)(C)C)N[Si](C)(C)C	standard polar	2025-10-24	1421.62
Gas Chromatography	(2R,4S)-2,4-diaminopentanoic acid_TMS_10	C[C@@H](C[C@@H](N)C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C	standard polar	2025-10-24	2161.26
Gas Chromatography	(2R,4S)-2,4-diaminopentanoic acid_TMS_11	C[C@H](N)C[C@H](C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C	standard polar	2025-10-24	3035.54
Gas Chromatography	(2R,4S)-2,4-diaminopentanoic acid_TMS_12	C[C@@H](C[C@H](C(=O)O)N([Si](C)(C)C)[Si](C)(C)C)N[Si](C)(C)C	standard polar	2025-10-24	2087.89
Gas Chromatography	(2R,4S)-2,4-diaminopentanoic acid_TMS_13	C[C@@H](C[C@@H](N[Si](C)(C)C)C(=O)O)N([Si](C)(C)C)[Si](C)(C)C	standard polar	2025-10-24	2249.33
Gas Chromatography	(2R,4S)-2,4-diaminopentanoic acid_TMS_14	C[C@@H](C[C@H](C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C)N[Si](C)(C)C	standard polar	2025-10-24	2022.94
Gas Chromatography	(2R,4S)-2,4-diaminopentanoic acid_TMS_15	C[C@@H](C[C@@H](N[Si](C)(C)C)C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C	standard polar	2025-10-24	2504.53
Gas Chromatography	(2R,4S)-2,4-diaminopentanoic acid_TMS_16	C[C@@H](C[C@H](C(=O)O)N([Si](C)(C)C)[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C	standard polar	2025-10-24	2111.28
Gas Chromatography	(2R,4S)-2,4-diaminopentanoic acid_TMS_17	C[C@@H](C[C@H](C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C	standard polar	2025-10-24	1949.37

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	Firmicutes	1	Human feces
Bacteria	nah	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

Not Available

KEGG Compound ID

C03943

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

440169

PDB ID

Not Available

ChEBI ID

4280

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 (2R,4S)-2,4-diaminopentanoic acid (MMDBc0054042)

MOL for #<Metabolite:0x00007f9acdd75900>

3D MOL for #<Metabolite:0x00007f9acdd75900>

3D SDF for #<Metabolite:0x00007f9acdd75900>

3D-SDF for #<Metabolite:0x00007f9acdd75900>

PDB for #<Metabolite:0x00007f9acdd75900>

3D PDB for #<Metabolite:0x00007f9acdd75900>

SMILES for #<Metabolite:0x00007f9acdd75900>

INCHI for #<Metabolite:0x00007f9acdd75900>

Structure for #<Metabolite:0x00007f9acdd75900>

3D Structure for #<Metabolite:0x00007f9acdd75900>