MiMeDB: Showing metabocard for 7,8-Diaminononanoate (MMDBc0030033)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:51:23 UTC

Update Date

2022-08-31 17:38:54 UTC

Metabolite ID

MMDBc0030033

Metabolite Identification

Common Name

7,8-Diaminononanoate

Description

7,8-diaminononanoate (or DAPA) is an intermediate in biotin biosynthesis. It is a substrate for Adenosylmethionine-8-amino-7-oxononanoate aminotransferase (or bioA). This enzyme catalyzes the transfer of the alpha-amino group from S-adenosyl-L-methionine (SAM) to 7-keto-8-aminopelargonic acid (KAPA) to form 7,8-diaminopelargonic acid (DAPA). The reaction is S-adenosyl-L-methionine + 8-amino-7-oxononanoate = S-adenosyl-4-methylthio-2-oxobutanoate + 7,8-diaminononanoate. DAPA is a simple intercalator, much like the widely studied 9-aminoacridine. (PMID 16180206 ; 16984394)

Structure

MOL SDF PDB SMILES InChI

HEADER    PROTEIN                                 15-MAY-15   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   15-MAY-15         0                                  
HETATM    1  C   UNK     0      -6.002  -0.385   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -4.668   0.385   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0      -4.668   1.925   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0      -3.334  -0.385   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0      -3.334  -1.925   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0      -2.001   0.385   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.667  -0.385   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.667   0.385   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.001  -0.385   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.334   0.385   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.668  -0.385   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       6.002   0.385   0.000  0.00  0.00           O-1
HETATM   13  O   UNK     0       4.668  -1.925   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   24    0
END

Synonyms

Value	Source
7,8-Diaminononanoic acid	Generator

Molecular Formula

C₉H₁₉N₂O₂

Average Mass

187.264

Monoisotopic Mass

187.14520144

IUPAC Name

7,8-diaminononanoate

Traditional Name

7,8-diaminononanoate

CAS Registry Number

21738-21-6

SMILES

CC(N)C(N)CCCCCC([O-])=O

InChI Identifier

InChI=1S/C9H20N2O2/c1-7(10)8(11)5-3-2-4-6-9(12)13/h7-8H,2-6,10-11H2,1H3,(H,12,13)/p-1

InChI Key

KCEGBPIYGIWCDH-UHFFFAOYSA-M

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as medium-chain fatty acids. These are fatty acids with an aliphatic tail that contains between 4 and 12 carbon atoms.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty acids and conjugates

Direct Parent

Medium-chain fatty acids

Alternative Parents

Substituents

Medium-chain fatty acid
Amino fatty acid
Branched fatty acid
Methyl-branched fatty acid
Amino acid or derivatives
Amino acid
Carboxylic acid derivative
Carboxylic acid
Monocarboxylic acid or derivatives
Amine
Organic nitrogen compound
Primary amine
Organooxygen compound
Organonitrogen compound
Primary aliphatic amine
Hydrocarbon derivative
Organic oxide
Carbonyl group
Organopnictogen compound
Organic oxygen compound
Organic anion
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

amino-acid anion (CHEBI:17830 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	15.5 g/L	ALOGPS
logP	0.31	ALOGPS
logP	-1.9	ChemAxon
logS	-1.1	ALOGPS
pKa (Strongest Acidic)	4.73	ChemAxon
pKa (Strongest Basic)	9.97	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	92.17 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	62.14 m³·mol⁻¹	ChemAxon
Polarizability	21.52 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	Deposition Date	View
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

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0007261	8-Amino-7-oxononanoate	S-Adenosyl-4-methylthio-2-oxobutanoate	Not Available	Adenosylmethionine-8-amino-7-oxononanoate transaminase	VMH	30371894
MMDBr0007301	Adenosine triphosphate	ADP	Not Available	Dethiobiotin synthase	VMH	30371894
MMDBr0018045	S-Adenosylmethionine	7,8-Diaminononanoate	Adenosylmethionine-8-amino-7-oxononanoate aminotransferase	Amine group addition	PathBank	31602464
MMDBr0018046	Carbon dioxide	Phosphate	ATP-dependent dethiobiotin synthetase BioD 1	Synthesis	PathBank	31602464

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	159	Human feces; Human sputum; Human ; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human feces; pleural fluid plaque; bal; Human stool	Unknown; Metabolic reconstruction
Bacteria	Firmicutes	123	Pig ; Human feces; Human	Metabolic reconstruction
Bacteria	Verrucomicrobia	1	Human ; Human feces	Metabolic reconstruction
Bacteria	Bacteroidetes	77	Human feces; Human ; Human stool; Human saliva; Human supragingival plaque; Human subgingival plaque	Metabolic reconstruction
Bacteria	Synergistetes	2	Human feces	Metabolic reconstruction
Bacteria	Actinobacteria	31	Human feces; Human	Metabolic reconstruction
Bacteria	Spirochaetes	1	Human feces	Metabolic reconstruction
Archaea	Thaumarchaeota	1		Metabolic reconstruction
Bacteria	Fusobacteria	18	Human feces; Human	Metabolic reconstruction
Archaea	Euryarchaeota	2		Metabolic reconstruction
Bacteria	Planctomycetes	1	Human feces	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

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

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5460128

PDB ID

Not Available

ChEBI ID

17830

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 ]

Showing metabocard for 7,8-Diaminononanoate (MMDBc0030033)

MOL for #<Metabolite:0x00007fa4b1771480>

3D MOL for #<Metabolite:0x00007fa4b1771480>

3D SDF for #<Metabolite:0x00007fa4b1771480>

3D-SDF for #<Metabolite:0x00007fa4b1771480>

PDB for #<Metabolite:0x00007fa4b1771480>

3D PDB for #<Metabolite:0x00007fa4b1771480>

SMILES for #<Metabolite:0x00007fa4b1771480>

INCHI for #<Metabolite:0x00007fa4b1771480>

Structure for #<Metabolite:0x00007fa4b1771480>

3D Structure for #<Metabolite:0x00007fa4b1771480>