Jump To Section:

Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References XML

Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-10 20:57:40 UTC

Update Date

2021-09-26 22:50:58 UTC

HMDB ID

HMDB0243725

Secondary Accession Numbers

None

Metabolite Identification

Common Name

(S)-Dimethyl 2-aminopentanedioate

Description

Dimethyl 2-aminopentanedioate belongs to the class of organic compounds known as glutamic acid and derivatives. Glutamic acid and derivatives are compounds containing glutamic acid or a derivative thereof resulting from reaction of glutamic acid at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. Dimethyl 2-aminopentanedioate is a very strong basic compound (based on its pKa). This compound has been identified in human blood as reported by (PMID: 31557052 ). (s)-dimethyl 2-aminopentanedioate is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically (S)-Dimethyl 2-aminopentanedioate is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.

Structure

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

HEADER    PROTEIN                                 18-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   18-APR-15         0                                  
HETATM    1  C   UNK     0       5.596   4.771   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       6.930   4.001   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       8.264   4.771   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       8.264   6.311   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       9.597   4.001   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      10.931   4.771   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      12.265   4.001   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0      12.265   2.461   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0      13.598   4.771   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      13.598   6.311   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      14.932   4.001   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      16.266   4.771   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12                                                       
CONECT   12   11                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   22    0
END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
Dimethyl 2-aminopentanedioic acid	Generator

Chemical Formula

C₇H₁₃NO₄

Average Molecular Weight

175.184

Monoisotopic Molecular Weight

175.084457903

IUPAC Name

1,5-dimethyl 2-aminopentanedioate

Traditional Name

1,5-dimethyl 2-aminopentanedioate

CAS Registry Number

Not Available

SMILES

COC(=O)CCC(N)C(=O)OC

InChI Identifier

InChI=1S/C7H13NO4/c1-11-6(9)4-3-5(8)7(10)12-2/h5H,3-4,8H2,1-2H3

InChI Key

YEJSPQZHMWGIGP-UHFFFAOYSA-N

Chemical Taxonomy

Description

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

Glutamic acid and derivatives

Alternative Parents

Substituents

Glutamic acid or derivatives
Alpha-amino acid ester
Fatty acid ester
Fatty acid methyl ester
Dicarboxylic acid or derivatives
Fatty acyl
Methyl ester
Carboxylic acid ester
Organic nitrogen compound
Organopnictogen compound
Primary amine
Organooxygen compound
Organonitrogen compound
Primary aliphatic amine
Organic oxygen compound
Carbonyl group
Amine
Hydrocarbon derivative
Organic oxide
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Source

Exogenous

Exogenous (PMID: 31557052)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	-0.55	ALOGPS
logP	-0.64	ChemAxon
logS	-0.28	ALOGPS
pKa (Strongest Basic)	7.38	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	78.62 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	40.83 m³·mol⁻¹	ChemAxon
Polarizability	17.79 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

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M+H]+	130.132	30932474
DeepCCS	[M-H]-	126.298	30932474
DeepCCS	[M-2H]-	163.738	30932474
DeepCCS	[M+Na]+	139.279	30932474
AllCCS	[M+H]+	141.1	32859911
AllCCS	[M+H-H2O]+	137.3	32859911
AllCCS	[M+NH4]+	144.6	32859911
AllCCS	[M+Na]+	145.7	32859911
AllCCS	[M-H]-	138.1	32859911
AllCCS	[M+Na-2H]-	139.7	32859911
AllCCS	[M+HCOO]-	141.7	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
(S)-Dimethyl 2-aminopentanedioate	COC(=O)CCC(N)C(=O)OC	2007.3	Standard polar	33892256
(S)-Dimethyl 2-aminopentanedioate	COC(=O)CCC(N)C(=O)OC	1295.1	Standard non polar	33892256
(S)-Dimethyl 2-aminopentanedioate	COC(=O)CCC(N)C(=O)OC	1348.9	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
(S)-Dimethyl 2-aminopentanedioate,1TMS,isomer #1	COC(=O)CCC(N[Si](C)(C)C)C(=O)OC	1405.2	Semi standard non polar	33892256
(S)-Dimethyl 2-aminopentanedioate,1TMS,isomer #1	COC(=O)CCC(N[Si](C)(C)C)C(=O)OC	1460.5	Standard non polar	33892256
(S)-Dimethyl 2-aminopentanedioate,1TMS,isomer #1	COC(=O)CCC(N[Si](C)(C)C)C(=O)OC	2053.9	Standard polar	33892256
(S)-Dimethyl 2-aminopentanedioate,2TMS,isomer #1	COC(=O)CCC(C(=O)OC)N([Si](C)(C)C)[Si](C)(C)C	1616.7	Semi standard non polar	33892256
(S)-Dimethyl 2-aminopentanedioate,2TMS,isomer #1	COC(=O)CCC(C(=O)OC)N([Si](C)(C)C)[Si](C)(C)C	1583.6	Standard non polar	33892256
(S)-Dimethyl 2-aminopentanedioate,2TMS,isomer #1	COC(=O)CCC(C(=O)OC)N([Si](C)(C)C)[Si](C)(C)C	1961.3	Standard polar	33892256
(S)-Dimethyl 2-aminopentanedioate,1TBDMS,isomer #1	COC(=O)CCC(N[Si](C)(C)C(C)(C)C)C(=O)OC	1618.2	Semi standard non polar	33892256
(S)-Dimethyl 2-aminopentanedioate,1TBDMS,isomer #1	COC(=O)CCC(N[Si](C)(C)C(C)(C)C)C(=O)OC	1688.6	Standard non polar	33892256
(S)-Dimethyl 2-aminopentanedioate,1TBDMS,isomer #1	COC(=O)CCC(N[Si](C)(C)C(C)(C)C)C(=O)OC	2131.2	Standard polar	33892256
(S)-Dimethyl 2-aminopentanedioate,2TBDMS,isomer #1	COC(=O)CCC(C(=O)OC)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2035.6	Semi standard non polar	33892256
(S)-Dimethyl 2-aminopentanedioate,2TBDMS,isomer #1	COC(=O)CCC(C(=O)OC)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2015.4	Standard non polar	33892256
(S)-Dimethyl 2-aminopentanedioate,2TBDMS,isomer #1	COC(=O)CCC(C(=O)OC)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2130.6	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - (S)-Dimethyl 2-aminopentanedioate GC-MS (Non-derivatized) - 70eV, Positive	splash10-067r-9400000000-c606ca05c00c00f63b64	2021-09-23	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (S)-Dimethyl 2-aminopentanedioate GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Dimethyl 2-aminopentanedioate 10V, Positive-QTOF	splash10-0170-5900000000-6096a69231057c39c410	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Dimethyl 2-aminopentanedioate 20V, Positive-QTOF	splash10-00lm-9300000000-0a2c082bbc5d66c90850	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Dimethyl 2-aminopentanedioate 40V, Positive-QTOF	splash10-0a4i-9000000000-6ded7bdb294d6447505d	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Dimethyl 2-aminopentanedioate 10V, Negative-QTOF	splash10-01ox-0900000000-016833f9777ac589a7ea	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Dimethyl 2-aminopentanedioate 20V, Negative-QTOF	splash10-03ec-6900000000-a268c09cbdef6c28a7f8	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Dimethyl 2-aminopentanedioate 40V, Negative-QTOF	splash10-0006-9000000000-c24e79fd97b5ae57bdbd	2021-10-12	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	31557052	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

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

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

416902

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

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 (S)-Dimethyl 2-aminopentanedioate (HMDB0243725)

MOL for HMDB0243725 ((S)-Dimethyl 2-aminopentanedioate)

3D MOL for HMDB0243725 ((S)-Dimethyl 2-aminopentanedioate)

3D SDF for HMDB0243725 ((S)-Dimethyl 2-aminopentanedioate)

3D-SDF for HMDB0243725 ((S)-Dimethyl 2-aminopentanedioate)

PDB for HMDB0243725 ((S)-Dimethyl 2-aminopentanedioate)

3D PDB for HMDB0243725 ((S)-Dimethyl 2-aminopentanedioate)

SMILES for HMDB0243725 ((S)-Dimethyl 2-aminopentanedioate)

INCHI for HMDB0243725 ((S)-Dimethyl 2-aminopentanedioate)

Structure for HMDB0243725 ((S)-Dimethyl 2-aminopentanedioate)

3D Structure for HMDB0243725 ((S)-Dimethyl 2-aminopentanedioate)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra