Milk Composition Database: Showing metabocard for Diaminopimelic acid (BMDB0001370)

Identification Taxonomy Physical properties Spectra Concentrations Links References XML

Show more...Show more...

Record Information

Version

1.0

Creation Date

2016-09-30 22:44:52 UTC

Update Date

2020-05-05 18:40:10 UTC

MCDB ID

BMDB0001370

Secondary Accession Numbers

BMDB01370

Metabolite Identification

Common Name

Diaminopimelic acid

Description

Diaminopimelic acid, also known as LL-2,6-diaminopimelate or acid, diaminopimelic, belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom. Diaminopimelic acid exists as a solid, very hydrophobic, practically insoluble (in water), and relatively neutral molecule. Diaminopimelic acid exists in all living species, ranging from bacteria to humans.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
(S,S)-2,6-Diaminopimelic acid	ChEBI
(S-(R,r))-2,6-diaminoheptanedioic acid	ChEBI
L,L-2,6-Diaminopimelic acid	ChEBI
LL-2,6-Diaminoheptanedioate	ChEBI
LL-2,6-Diaminopimelate	ChEBI
LL-2,6-Diaminopimelic acid	Kegg
(S,S)-2,6-Diaminopimelate	Generator
(S-(R,r))-2,6-diaminoheptanedioate	Generator
L,L-2,6-Diaminopimelate	Generator
LL-2,6-Diaminoheptanedioic acid	Generator
Diaminopimelate	Generator
( (R,s)-2,6-diamino-heptanedioate	HMDB
( (R,s)-2,6-diamino-heptanedioic acid	HMDB
(2R,6S)-2,6-diamino-Heptanedioate	HMDB
(2R,6S)-2,6-diamino-Heptanedioic acid	HMDB
(R,s)-2,6-diamino-heptanedioate	HMDB
(R,s)-2,6-diamino-heptanedioic acid	HMDB
2,6-diamino-Heptanedioate	HMDB
2,6-diamino-Heptanedioic acid	HMDB
2,6-Diaminoheptanedioate	HMDB
2,6-Diaminoheptanedioic acid	HMDB
2,6-Diaminopimelate	HMDB
2,6-Diaminopimelic acid	HMDB, MeSH
a,A'-diaminopimelate	HMDB
a,A'-diaminopimelic acid	HMDB
a,e-Diaminopimelate	HMDB
a,e-Diaminopimelic acid	HMDB
D,L-Diaminopimelate	HMDB
D,L-meso-Diaminoheptanedioate	HMDB
D,L-meso-Diaminoheptanedioic acid	HMDB
DAPA	HMDB
DL-2,6-Diaminoheptanedioate	HMDB
DL-2,6-Diaminoheptanedioic acid	HMDB
DL-2,6-Diaminopimelate	HMDB
DL-2,6-Diaminopimelic acid	HMDB
L,L-2,6-Diaminoheptanedioate	HMDB
L,L-2,6-Diaminoheptanedioic acid	HMDB
L,L-Diaminopimelate	HMDB
meso-1-alpha,epsilon-Diaminopimelate	HMDB
meso-2,6-diamino-Heptanedioate	HMDB
meso-2,6-diamino-Heptanedioic acid	HMDB
meso-2,6-Diaminoheptanedioate	HMDB
meso-2,6-Diaminoheptanedioic acid	HMDB
meso-alpha,Alpha'-diaminopimelate	HMDB
meso-alpha,Alpha'-diaminopimelic acid	HMDB
meso-alpha,epsilon-Diaminopimelate	HMDB
meso-alpha,epsilon-Diaminopimelic acid	HMDB
meso-Diaminoheptanedioate	HMDB
meso-Diaminoheptanedioic acid	HMDB
meso-Diaminopimelate	HMDB
Acid, diaminopimelic	MeSH, HMDB
2,6 Diaminopimelic acid	MeSH, HMDB
Acid, 2,6-diaminopimelic	MeSH, HMDB
Diamino-pimelate	Generator, HMDB
Diaminopimelic acid	MeSH

Chemical Formula

C₇H₁₄N₂O₄

Average Molecular Weight

190.1971

Monoisotopic Molecular Weight

190.095356946

IUPAC Name

(2S,6S)-2,6-diaminoheptanedioic acid

Traditional Name

diamino-pimelic acid

CAS Registry Number

583-93-7

SMILES

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

InChI Identifier

InChI=1S/C7H14N2O4/c8-4(6(10)11)2-1-3-5(9)7(12)13/h4-5H,1-3,8-9H2,(H,10,11)(H,12,13)/t4-,5-/m0/s1

InChI Key

GMKMEZVLHJARHF-WHFBIAKZSA-N

Chemical Taxonomy

Description

belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-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

L-alpha-amino acids

Alternative Parents

Substituents

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

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

2,6-diaminopimelic acid (CHEBI:16026 )
Dicarboxylic acids (LMFA01170102 )

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	300 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	-4.1	ALOGPS
logP	-5.5	ChemAxon
logS	-1.1	ALOGPS
pKa (Strongest Acidic)	1.85	ChemAxon
pKa (Strongest Basic)	9.83	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	126.64 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	43.64 m³·mol⁻¹	ChemAxon
Polarizability	18.93 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	1	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
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (4 TMS)	splash10-0umi-1950000000-749403a0eb6d05c7903e	2014-06-16	View Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (4 TMS)	splash10-0uk9-1980000000-1b092f9141e7549bee24	2014-06-16	View Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0umi-1950000000-749403a0eb6d05c7903e	2017-09-12	View Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0uk9-1980000000-1b092f9141e7549bee24	2017-09-12	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-00dm-9500000000-5d0aafd0747a1090e055	2016-09-22	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positive	splash10-014i-4590000000-b941e92697a8b7800912	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
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-004l-0900000000-d85213bd7ac426f10cd7	2012-07-24	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-001i-9100000000-add590f1b216bdb40334	2012-07-24	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-001i-9000000000-de98ed3bb8c48b6f9852	2012-07-24	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 10V, Positive	splash10-004i-0900000000-2c8a0ca138ef6ea5ef43	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 20V, Positive	splash10-003r-9600000000-19f54d2417fe44d0eba3	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 10V, Negative	splash10-000i-0900000000-e8b0bbffeaa501a6fedd	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 40V, Positive	splash10-0a4i-9000000000-91296097628a67dd97ef	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 40V, Positive	splash10-0a4i-9000000000-e5c4e034dcab0695e0ce	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 35V, Negative	splash10-002r-0900000000-2a19445fee9eade1d538	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 40V, Negative	splash10-00di-9000000000-f44538bc8ae3a51cbbc6	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 20V, Positive	splash10-003r-9700000000-3baa36a29b4ed6172da0	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 10V, Positive	splash10-004i-1900000000-cf39d89ce72ac9ddaf51	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 20V, Negative	splash10-0200-6900000000-6f21b7798408480c1bfc	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 20V, Positive	splash10-001i-9300000000-6e778092666f89ff4211	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 10V, Positive	splash10-004i-0900000000-28fbb202ae5558af7594	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 35V, Positive	splash10-004i-1900000000-8a1ee3da7fbe94f840c2	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 40V, Positive	splash10-0a4i-9000000000-8caae42eda716644fdc1	2021-09-20	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0005-1900000000-be94a16bee7fad24d5d9	2016-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0002-5900000000-896859ce722942f9dd68	2016-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-006t-9200000000-50c1b5a4f7b19e8ff0db	2016-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-000i-0900000000-5ecd829b51ba774883f6	2016-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-000i-1900000000-53b7aee01233b5b73d3e	2016-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-00di-9400000000-2cc35eb21a44b2d472b5	2016-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0079-0900000000-a0ce1f9601e9b8d83ccf	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-00dj-6900000000-cc22f522673c5549366c	2021-09-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, experimental)	Not Available	2012-12-04	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)	Not Available	2012-12-05	View Spectrum

Concentrations

Status	Value		Reference	Details
Detected but not Quantified	Not Applicable		PMID: 28306241	details
Detected but not Quantified	Not Applicable		PMID: 29291809	details

External Links

HMDB ID

HMDB0001370

DrugBank ID

DB03590

Phenol Explorer Compound ID

Not Available

FoodDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Not Available

Wikipedia Link

Diaminopimelic acid

METLIN ID

352

PubChem Compound

439283

PDB ID

Not Available

ChEBI ID

16026

References

Synthesis Reference

Gao, Yong. Synthesis of diaminopimelic acid (DAP) and analogues: mechanistic studies on DAP aminotransferase, epimerase and dehydrogenase. (1998), 166 pp.

Material Safety Data Sheet (MSDS)

Download (PDF)

General References

Mung D, Li L: Development of Chemical Isotope Labeling LC-MS for Milk Metabolomics: Comprehensive and Quantitative Profiling of the Amine/Phenol Submetabolome. Anal Chem. 2017 Apr 18;89(8):4435-4443. doi: 10.1021/acs.analchem.6b03737. Epub 2017 Mar 28. [PubMed:28306241 ]
Mung D, Li L: Applying quantitative metabolomics based on chemical isotope labeling LC-MS for detecting potential milk adulterant in human milk. Anal Chim Acta. 2018 Feb 25;1001:78-85. doi: 10.1016/j.aca.2017.11.019. Epub 2017 Nov 14. [PubMed:29291809 ]

Showing metabocard for Diaminopimelic acid (BMDB0001370)

Structure for BMDB0001370 (Diaminopimelic acid)