MiMeDB: Showing metabocard for (3S,5S)-3,5-Diaminocaproate (MMDBc0049859)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-04-29 22:44:56 UTC

Update Date

2022-09-01 02:16:40 UTC

Metabolite ID

MMDBc0049859

Metabolite Identification

Common Name

(3S,5S)-3,5-Diaminocaproate

Description

(3S,5S)-3,5-Diaminohexanoate, also known as (3S,5S)-3,5-diaminocaproic acid or L-erythro-3,5-diaminohexanoate, belongs to the class of organic compounds known as beta amino acids and derivatives. These are amino acids having a (-NH2) group attached to the beta carbon atom (3S,5S)-3,5-Diaminohexanoate exists in all living organisms, ranging from bacteria to humans (3S,5S)-3,5-Diaminohexanoate has been detected, but not quantified in, a few different foods, such as anatidaes (Anatidae), chickens (Gallus gallus), and domestic pigs (Sus scrofa domestica). This could make (3S,5S)-3,5-diaminohexanoate a potential biomarker for the consumption of these foods (3S,5S)-3,5-Diaminohexanoate is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review very few articles have been published on (3S,5S)-3,5-Diaminohexanoate.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

Synonyms

Value	Source
(3S,5S)-3,5-Diaminocaproic acid	ChEBI
L-Erythro-3,5-diaminohexanoic acid	ChEBI
L-Erythro-3,5-diaminohexanoate	Kegg
(3S,5S)-3,5-Diaminocaproate	Kegg
L-Erythro-3,5-diaminocaproate	Kegg
L-Erythro-3,5-diaminocaproic acid	Generator
(3S,5S)-3,5-Diaminohexanoic acid	Generator
3,5-diamino-Hexanoate	HMDB
3,5-diamino-Hexanoic acid	HMDB
3,5-Diaminohexanoate	HMDB
3,5-Diaminohexanoic acid	HMDB
(3S,5S)-3,5-Diaminohexanoate	Generator
3,5-Diaminohexanoate dihydrochloride	MeSH, HMDB

Molecular Formula

C₆H₁₄N₂O₂

Average Mass

146.1876

Monoisotopic Mass

146.105527702

IUPAC Name

(3S,5S)-3,5-diaminohexanoic acid

Traditional Name

L-erythro-3,5-diaminohexanoate

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C6H14N2O2/c1-4(7)2-5(8)3-6(9)10/h4-5H,2-3,7-8H2,1H3,(H,9,10)/t4-,5-/m0/s1

InChI Key

NGDLSXMSQYUVSJ-WHFBIAKZSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as beta amino acids and derivatives. These are amino acids having a (-NH2) group attached to the beta 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

Beta amino acids and derivatives

Alternative Parents

Substituents

Beta amino acid or derivatives
Medium-chain fatty acid
Amino fatty acid
Fatty acid
Fatty acyl
Amino acid
Carboxylic acid
Monocarboxylic acid or derivatives
Organopnictogen compound
Primary amine
Organooxygen compound
Organonitrogen compound
Amine
Primary aliphatic amine
Carbonyl group
Organic oxygen compound
Organic nitrogen compound
Organic oxide
Hydrocarbon derivative
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

beta-amino acid (CHEBI:15616 )
diamino acid (CHEBI:15616 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	126 g/L	ALOGPS
logP	-3.5	ALOGPS
logP	-3.5	ChemAxon
logS	-0.06	ALOGPS
pKa (Strongest Acidic)	4.25	ChemAxon
pKa (Strongest Basic)	10.75	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	4	ChemAxon
Refractivity	37.61 m³·mol⁻¹	ChemAxon
Polarizability	15.58 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	splash10-000l-9000000000-fe616d85bb79ec3ff09c	2017-09-01	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	splash10-0006-9500000000-37d2c2ce4f47617362dd	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
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03gj-0900000000-1ac1f45f87957708533b	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0239-8900000000-82cfe4ca274f38ceb15b	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-06si-9200000000-cb1115634f2f540cbdc5	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0002-0900000000-a0d8c37141bc7dc8c935	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0ufs-2900000000-ef10441acee32815ad0d	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-053u-9300000000-af983005a00ac2fc75ae	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-001r-7900000000-93da6a650a515a8a47f5	2021-09-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-01q9-9400000000-66b0a498aeff05bec142	2021-09-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-00dl-9000000000-4a46b2c4530c64cfddde	2021-09-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-004i-5900000000-6d6ff3949d0dc471dc59	2021-09-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004l-8900000000-4a00612c8074ae2c39d1	2021-09-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9000000000-86e204bc007aae592616	2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-25	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

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0006890	(3S)-3,6-Diaminohexanoate	(3S,5S)-3,5-Diaminocaproate	Not Available	(3S)-3,6-Diaminohexanoate 5,6-aminomutase	VMH	30371894
MMDBr0007002	(3S,5S)-3,5-Diaminocaproate	(S)-5-Amino-3-oxohexanoate	Not Available	L-3,5-diaminohexanoate dehydrogenase	VMH	30371894
MMDBr0013903	(3S,5S)-3,5-Diaminocaproate	(S)-5-Amino-3-oxohexanoate	L-erythro-3,5-diaminohexanoate dehydrogenase	Dehydrogenation	RHEA	34755880
MMDBr0014139	(3S)-3,6-Diaminohexanoate	(3S,5S)-3,5-Diaminocaproate	Lysine 5,6-aminomutase alpha subunit	Non-hydrolytic bond cleavage (or its reversal)	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
Bacteria	Bacteroidetes	12	Human feces; Human	Metabolic reconstruction
Bacteria	Actinobacteria	2	Human feces	Metabolic reconstruction
Bacteria	Fusobacteria	19	Human feces; Human	Metabolic reconstruction
Bacteria	Firmicutes	6	Human feces; Human	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

HMDB0012115

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB028779

KNApSAcK ID

Not Available

Chemspider ID

388540

KEGG Compound ID

C01186

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

439430

PDB ID

Not Available

ChEBI ID

15616

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Noronha A, Modamio J, Jarosz Y, Guerard E, Sompairac N, Preciat G, Danielsdottir AD, Krecke M, Merten D, Haraldsdottir HS, Heinken A, Heirendt L, Magnusdottir S, Ravcheev DA, Sahoo S, Gawron P, Friscioni L, Garcia B, Prendergast M, Puente A, Rodrigues M, Roy A, Rouquaya M, Wiltgen L, Zagare A, John E, Krueger M, Kuperstein I, Zinovyev A, Schneider R, Fleming RMT, Thiele I: The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Res. 2019 Jan 8;47(D1):D614-D624. doi: 10.1093/nar/gky992. [PubMed:30371894 ]
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 (3S,5S)-3,5-Diaminocaproate (MMDBc0049859)

MOL for #<Metabolite:0x00007fe2d5327868>

3D MOL for #<Metabolite:0x00007fe2d5327868>

3D SDF for #<Metabolite:0x00007fe2d5327868>

3D-SDF for #<Metabolite:0x00007fe2d5327868>

PDB for #<Metabolite:0x00007fe2d5327868>

3D PDB for #<Metabolite:0x00007fe2d5327868>

SMILES for #<Metabolite:0x00007fe2d5327868>

INCHI for #<Metabolite:0x00007fe2d5327868>

Structure for #<Metabolite:0x00007fe2d5327868>

3D Structure for #<Metabolite:0x00007fe2d5327868>