MiMeDB: Showing metabocard for N-Formyl-4-amino-5-aminomethyl-2-methylpyrimidine (MMDBc0053475)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-05-16 21:25:43 UTC

Update Date

2025-10-07 16:08:19 UTC

Metabolite ID

MMDBc0053475

Metabolite Identification

Common Name

N-Formyl-4-amino-5-aminomethyl-2-methylpyrimidine

Description

N-Formyl-4-amino-5-aminomethyl-2-methylpyrimidine is a metabolite belonging to the class of pyrimidines, specifically a degradation product of vitamin B1. Its chemical structure features a formyl group attached to a pyrimidine ring, which is further substituted with amino and aminomethyl groups, contributing to its reactivity and biological roles. FAMP is involved in the cycling of vitamin B1 in marine ecosystems, where it serves as an alternative source of vitamin B1 for various marine microbes, including bacteria and phytoplankton, thereby playing a crucial role in nutrient dynamics (PMID:37377416 ). Additionally, it is transported into cells via the ThiXYZ transport system and subsequently processed by the ylmB-encoded amidohydrolase, leading to the formation of 4-amino-5-hydroxymethyl-2-methylpyrimidine, an intermediate in the de novo thiamin biosynthetic pathway (PMID:17618314 ). This pathway highlights the importance of FAMP in microbial metabolism and its potential implications in plant oxidative stress research, as its degradation products remain underexplored (PMID:37377416 ). Overall, N-formyl-4-amino-5-aminomethyl-2-methylpyrimidine exemplifies the intricate connections between chemical structure, metabolic pathways, and ecological interactions.

Structure

MOL SDF PDB SMILES InChI

HEADER    PROTEIN                                 04-MAY-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-MAY-14         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  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   11  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   12  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    5                                                            
CONECT    2    6    9                                                       
CONECT    3    6   10                                                       
CONECT    4    9   12                                                       
CONECT    5    1   10   11                                                  
CONECT    6    2    3    7                                                  
CONECT    7    6    8   11                                                  
CONECT    8    7                                                            
CONECT    9    2    4                                                       
CONECT   10    3    5                                                       
CONECT   11    5    7                                                       
CONECT   12    4                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   24    0
END

Synonyms

Value	Source
2-Methyl-4-amino-5-(formylaminomethyl)pyrimidine	ChEBI
2-Methyl-4-amino-5-formylaminomethylpyrimidine	ChEBI
FAMP	ChEBI
N-[(4-Azanyl-2-methyl-pyrimidin-5-yl)methyl]methanamide	ChEBI
N-Formyl-4-amino-5-aminomethyl-2-methylpyrimidine	ChEBI

Molecular Formula

C₇H₁₀N₄O

Average Mass

166.1805

Monoisotopic Mass

166.085460962

IUPAC Name

N-[(6-imino-2-methyl-1,6-dihydropyrimidin-5-yl)methyl]carboximidic acid

Traditional Name

N-[(4-imino-2-methyl-3H-pyrimidin-5-yl)methyl]carboximidic acid

CAS Registry Number

Not Available

SMILES

CC1=NC=C(CN=CO)C(=N)N1

InChI Identifier

InChI=1S/C7H10N4O/c1-5-10-3-6(2-9-4-12)7(8)11-5/h3-4H,2H2,1H3,(H,9,12)(H2,8,10,11)

InChI Key

PVWNFAGYFUUDRC-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as aminopyrimidines and derivatives. These are organic compounds containing an amino group attached to a pyrimidine ring. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Diazines

Sub Class

Pyrimidines and pyrimidine derivatives

Direct Parent

Aminopyrimidines and derivatives

Alternative Parents

Substituents

Aminopyrimidine
Imidolactam
Heteroaromatic compound
Amino acid or derivatives
Carboxamide group
Secondary carboxylic acid amide
Carboxylic acid derivative
Azacycle
Amine
Hydrocarbon derivative
Primary amine
Organooxygen compound
Organonitrogen compound
Organic oxide
Organopnictogen compound
Carbonyl group
Organic oxygen compound
Organic nitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

aminopyrimidine (CHEBI:85895 )
formamides (CHEBI:85895 )
a pyrimidine-related compound (CPD-13577 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.3 g/L	ALOGPS
logP	-0.63	ALOGPS
logP	-1.3	ChemAxon
logS	-2.8	ALOGPS
pKa (Strongest Acidic)	3.83	ChemAxon
pKa (Strongest Basic)	12.21	ChemAxon
Physiological Charge	2	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	80.83 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	55.09 m³·mol⁻¹	ChemAxon
Polarizability	16.8 Å³	ChemAxon
Number of Rings	1	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_1_3) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	Not Available	2022-08-09	View Spectrum
MS	Mass Spectrum (Electron Ionization)	Not Available	2022-08-06	View Spectrum

Chromatographic Retention Times and Retention Indices

Retention Times

Chromatography Type	Technique	Column	Deposition Date	Retention Time (s)
Liquid Chromatography	HILIC	Waters Acquity UPLC-BEH Amide column (eluted)	2025-10-24	354.6
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-24	301.8
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (void)	2025-10-24	38.6
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-24	226.4
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-24	267.5
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (void)	2025-10-24	269.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	479.1
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	756.8
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-24	552.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	148.2
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	420.5
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	162.0
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	61.9
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	375.9
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	507.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	45.8
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	172.8
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-24	756.8
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-24	561.6

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	N-Formyl-4-amino-5-aminomethyl-2-methylpyrimidine_TMS_1	CC1=NC=C(CN=CO[Si](C)(C)C)C(=N)[NH]1	standard non polar	2025-10-24	2193.04
Gas Chromatography	N-Formyl-4-amino-5-aminomethyl-2-methylpyrimidine_TMS_2	CC1=NC=C(CN=CO)C(=N[Si](C)(C)C)[NH]1	standard non polar	2025-10-24	2482.66
Gas Chromatography	N-Formyl-4-amino-5-aminomethyl-2-methylpyrimidine_TMS_3	CC1=NC=C(CN=CO)C(=N)N1[Si](C)(C)C	standard non polar	2025-10-24	1919.69
Gas Chromatography	N-Formyl-4-amino-5-aminomethyl-2-methylpyrimidine_TMS_4	CC1=NC=C(CN=CO[Si](C)(C)C)C(=N[Si](C)(C)C)[NH]1	standard non polar	2025-10-24	1948.55
Gas Chromatography	N-Formyl-4-amino-5-aminomethyl-2-methylpyrimidine_TMS_5	CC1=NC=C(CN=CO[Si](C)(C)C)C(=N)N1[Si](C)(C)C	standard non polar	2025-10-24	2732.01
Gas Chromatography	N-Formyl-4-amino-5-aminomethyl-2-methylpyrimidine_TMS_6	CC1=NC=C(CN=CO)C(=N[Si](C)(C)C)N1[Si](C)(C)C	standard non polar	2025-10-24	2328.79
Gas Chromatography	N-Formyl-4-amino-5-aminomethyl-2-methylpyrimidine_TMS_7	CC1=NC=C(CN=CO[Si](C)(C)C)C(=N[Si](C)(C)C)N1[Si](C)(C)C	standard non polar	2025-10-24	1668.1
Gas Chromatography	N-Formyl-4-amino-5-aminomethyl-2-methylpyrimidine_TMS_1	CC1=NC=C(CN=CO[Si](C)(C)C)C(=N)[NH]1	standard polar	2025-10-24	2097.53
Gas Chromatography	N-Formyl-4-amino-5-aminomethyl-2-methylpyrimidine_TMS_2	CC1=NC=C(CN=CO)C(=N[Si](C)(C)C)[NH]1	standard polar	2025-10-24	2159.62
Gas Chromatography	N-Formyl-4-amino-5-aminomethyl-2-methylpyrimidine_TMS_3	CC1=NC=C(CN=CO)C(=N)N1[Si](C)(C)C	standard polar	2025-10-24	1788.14
Gas Chromatography	N-Formyl-4-amino-5-aminomethyl-2-methylpyrimidine_TMS_4	CC1=NC=C(CN=CO[Si](C)(C)C)C(=N[Si](C)(C)C)[NH]1	standard polar	2025-10-24	2781.83
Gas Chromatography	N-Formyl-4-amino-5-aminomethyl-2-methylpyrimidine_TMS_5	CC1=NC=C(CN=CO[Si](C)(C)C)C(=N)N1[Si](C)(C)C	standard polar	2025-10-24	2336.37
Gas Chromatography	N-Formyl-4-amino-5-aminomethyl-2-methylpyrimidine_TMS_6	CC1=NC=C(CN=CO)C(=N[Si](C)(C)C)N1[Si](C)(C)C	standard polar	2025-10-24	2232.23
Gas Chromatography	N-Formyl-4-amino-5-aminomethyl-2-methylpyrimidine_TMS_7	CC1=NC=C(CN=CO[Si](C)(C)C)C(=N[Si](C)(C)C)N1[Si](C)(C)C	standard polar	2025-10-24	2248.81

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

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

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

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/Eubacteria	Firmicutes	2	Human feces

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

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

C19872

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

597195

PDB ID

Not Available

ChEBI ID

85895

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

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 N-Formyl-4-amino-5-aminomethyl-2-methylpyrimidine (MMDBc0053475)

MOL for #<Metabolite:0x00007f9aa62db160>

3D MOL for #<Metabolite:0x00007f9aa62db160>

3D SDF for #<Metabolite:0x00007f9aa62db160>

3D-SDF for #<Metabolite:0x00007f9aa62db160>

PDB for #<Metabolite:0x00007f9aa62db160>

3D PDB for #<Metabolite:0x00007f9aa62db160>

SMILES for #<Metabolite:0x00007f9aa62db160>

INCHI for #<Metabolite:0x00007f9aa62db160>

Structure for #<Metabolite:0x00007f9aa62db160>

3D Structure for #<Metabolite:0x00007f9aa62db160>