MiMeDB: Showing metabocard for Meso-2,6-Diaminoheptanedioate (MMDBc0031728)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 01:46:05 UTC

Update Date

2022-08-31 18:23:59 UTC

Metabolite ID

MMDBc0031728

Metabolite Identification

Common Name

Meso-2,6-Diaminoheptanedioate

Description

Meso-2,6-diaminoheptanedioate is a member of the chemical class known as Alpha Amino Acids and Derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon). This particular compound is at a branch point in lysine biosynthesis where it is either the penultimate step in lysine biosynthesis in E. coli (via diaminopimelate decarboxylase, LysA) or it can be directed towards the synthesis of peptidoglycan (via murE).

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 10191209532D          

 15 14  0  0  0  0            999 V2000
    5.8559    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1414    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5704    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4270    2.5559    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.2849    2.5559    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.7125    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9993    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4270    3.3809    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.2849    3.3809    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9980    2.5559    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125    1.3184    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.7138    2.5559    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.9993    1.3184    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4270    1.7309    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2849    1.7309    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  0  0  0  0
  7  5  1  0  0  0  0
  4  8  1  6  0  0  0
  5  9  1  6  0  0  0
 10  6  2  0  0  0  0
 11  6  1  0  0  0  0
 12  7  2  0  0  0  0
 13  7  1  0  0  0  0
  4 14  1  6  0  0  0
  5 15  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0031728

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@](N)(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+

> <INCHI_KEY>
GMKMEZVLHJARHF-SYDPRGILSA-N

> <FORMULA>
C7H14N2O4

> <MOLECULAR_WEIGHT>
190.1971

> <EXACT_MASS>
190.095356946

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
18.68414320863363

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,6S)-2,6-diaminoheptanedioic acid

> <ALOGPS_LOGP>
-4.13

> <JCHEM_LOGP>
-5.545367993935247

> <ALOGPS_LOGS>
-1.13

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
2.585040505515713

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.8470749826619342

> <JCHEM_PKA_STRONGEST_BASIC>
9.827564769536531

> <JCHEM_POLAR_SURFACE_AREA>
126.64

> <JCHEM_REFRACTIVITY>
43.6394

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.41e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
diaminopimelic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 19-OCT-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-OCT-12         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM    9  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   10  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   14  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   15  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    5                                                       
CONECT    4    2    6    8   14                                             
CONECT    5    3    7    9   15                                             
CONECT    6    4   10   11                                                  
CONECT    7    5   12   13                                                  
CONECT    8    4                                                            
CONECT    9    5                                                            
CONECT   10    6                                                            
CONECT   11    6                                                            
CONECT   12    7                                                            
CONECT   13    7                                                            
CONECT   14    4                                                            
CONECT   15    5                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   28    0
END

Synonyms

Value	Source
Meso-diaminoheptanedioic acid	ChEBI
Meso-2,6-diaminopimelate	Kegg
Meso-2,6-diaminopimelic acid	Kegg
Meso-diaminoheptanedioate	Kegg
Meso-diaminopimelic acid	Generator
meso-2,6-Diaminoheptanedioic acid	Generator

Molecular Formula

C₇H₁₄N₂O₄

Average Mass

190.1971

Monoisotopic Mass

190.095356946

IUPAC Name

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

Traditional Name

diaminopimelic acid

CAS Registry Number

922-54-3

SMILES

[H][C@](N)(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+

InChI Key

GMKMEZVLHJARHF-SYDPRGILSA-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

D-alpha-amino acid
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
Organic oxide
Hydrocarbon derivative
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

2,6-diaminopimelic acid (CHEBI:16488 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	14.1 g/L	ALOGPS
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	18.68 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_2_2) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-006w-1900000000-b0e4598bfac1f1042028	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0002-5900000000-3cf670544958e8c5e216	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-006t-9200000000-cb92e651126ece5c413e	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-000i-0900000000-c81ad78d33d56b184c0a	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0079-1900000000-be9446a41a29ccfe478c	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-00di-9500000000-737f0f27e617ae2e898e	2015-09-15	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-18	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

Reactions

Reaction ID	Precursor	Product	Enzyme	Data Source	Reference
MMDBr0007299	Meso-2,6-Diaminoheptanedioate	L-Lysine	Not Available	VMH	30371894
MMDBr0007300	LL-2,6-Diaminoheptanedioate	Meso-2,6-Diaminoheptanedioate	Not Available	VMH	30371894
MMDBr0007586	Meso-2,6-Diaminoheptanedioate	UDP-N-Acetylmuramoyl-L-alanyl-D-gamma-glutamyl-meso-2,6-diaminopimelate	Not Available	VMH	30371894
MMDBr0011006	2,3,4,5-Tetrahydrodipicolinate	Meso-2,6-Diaminoheptanedioate	Not Available	VMH	30371894

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	Proteobacteria	456	Human ; Human feces; Human sputum; Human unknown; Human pleural fluid plaque; Pig ; Human dental plaque; Human nasal swab; Human stool; Human feces; pleural fluid plaque; bal; Human subgingival plaque; Cattle ; River trout ; Rat ; Sheep ; Chicken ; American dog tick	Unknown; Metabolic reconstruction
Bacteria	Actinobacteria	150	Human feces; Human pleural fluid plaque; Human dental plaque; Human sputum; Human ; Human supragingival plaque; Human mucosa; Human subgingival plaque; Human nasopharyngeal swab; Human saliva; Cattle	Metabolic reconstruction
Bacteria	Verrucomicrobia	1	Human ; Human feces	Metabolic reconstruction
Bacteria	Bacteroidetes	119	Human feces; Human appendix biopsy; Human ; Human stool; Human saliva; Human gastric fluid; Human urine; Human supragingival plaque; Human subgingival plaque	Metabolic reconstruction
Bacteria	Firmicutes	415	Human feces; Human ; Human stool; Human saliva; Human pleural fluid plaque; Pig ; Human subgingival plaque; Cattle ; Catfish	Metabolic reconstruction
Bacteria	Fusobacteria	19	Human feces; Human	Metabolic reconstruction
Archaea	Euryarchaeota	5		Metabolic reconstruction
Bacteria	Synergistetes	3	Human feces	Metabolic reconstruction
Bacteria	Spirochaetes	7	Human feces; Pig ; Human	Metabolic reconstruction
Archaea	Thaumarchaeota	1		Metabolic reconstruction
Bacteria	Planctomycetes	1	Human feces	Metabolic reconstruction
Archaea	Crenarchaeota	1		Metabolic reconstruction
Bacteria	Tenericutes	2	Human feces	Metabolic reconstruction
Bacteria	Aquificae	2
Archaea/Archaea	Euryarchaeota	12		Metabolic reconstruction
Bacteria	Deinococcus-thermus	1
Bacteria	nah	1
Bacteria	Thermotogae	1
Bacteria	Cyanobacteria	24	Human
Bacteria	Chlamydiae	9	Human ; Sheep ; Cat
Bacteria	Chlorobi	2
Bacteria	Elusimicrobia	1
Bacteria	Gemmatimonadetes	1
Bacteria	Acidobacteria	1

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

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

C00007595

Chemspider ID

Not Available

KEGG Compound ID

C00680

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Diaminopimelic_acid

METLIN ID

Not Available

PubChem Compound

99290

PDB ID

Not Available

ChEBI ID

16488

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 ]
Wishart DS, Li C, Marcu A, Badran H, Pon A, Budinski Z, Patron J, Lipton D, Cao X, Oler E, Li K, Paccoud M, Hong C, Guo AC, Chan C, Wei W, Ramirez-Gaona M: PathBank: a comprehensive pathway database for model organisms. Nucleic Acids Res. 2020 Jan 8;48(D1):D470-D478. doi: 10.1093/nar/gkz861. [PubMed:31602464 ]
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 Meso-2,6-Diaminoheptanedioate (MMDBc0031728)

MOL for #<Metabolite:0x00007fed15880b30>

3D MOL for #<Metabolite:0x00007fed15880b30>

3D SDF for #<Metabolite:0x00007fed15880b30>

3D-SDF for #<Metabolite:0x00007fed15880b30>

PDB for #<Metabolite:0x00007fed15880b30>

3D PDB for #<Metabolite:0x00007fed15880b30>

SMILES for #<Metabolite:0x00007fed15880b30>

INCHI for #<Metabolite:0x00007fed15880b30>

Structure for #<Metabolite:0x00007fed15880b30>

3D Structure for #<Metabolite:0x00007fed15880b30>