MiMeDB: Showing metabocard for 4-Amino-5-aminomethyl-2-methylpyrimidine (MMDBc0051920)

Pharmaceutical

Xenobiotic

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-05-16 20:40:07 UTC

Update Date

2025-10-07 16:08:17 UTC

Metabolite ID

MMDBc0051920

Metabolite Identification

Common Name

4-Amino-5-aminomethyl-2-methylpyrimidine

Description

4-Amino-5-aminomethyl-2-methylpyrimidine is a pyrimidine derivative involved in thiamine (vitamin B1) metabolism. It plays a crucial role in the salvage pathways that recycle thiamine breakdown products, particularly in marine microbial communities. This compound is utilized by eukaryotic phytoplankton and bacterioplankton, which can metabolize it to meet their vitamin B1 requirements, especially in nutrient-limited environments (PMID:37377416 ). The enzymatic hydrolysis of 4-amino-5-aminomethyl-2-methylpyrimidine by TenA proteins facilitates the conversion to 4-amino-5-hydroxymethyl-2-methylpyrimidine, a key intermediate in thiamine biosynthesis (PMID:25014715 , PMID:18054064 ). Additionally, it is noted that this compound, alongside its degradation products, contributes to the cycling of vitamin B1 in marine ecosystems, highlighting its ecological significance (PMID:38390520 ). The compound's involvement in plant oxidative stress research also suggests potential interactions in broader biological contexts (PMID:37377416 ). Overall, 4-amino-5-aminomethyl-2-methylpyrimidine serves as a vital metabolite in both microbial and ecological processes related to thiamine utilization.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
2-Methyl-4-amino-5-aminomethylpyrimidine	ChEBI
4-Amino-2-methylpyrimidine-5-methylamine	ChEBI
Amino-HMP	Kegg
4-amino-5-Aminomethyl-2-methylpyrimidine	MeSH

Molecular Formula

C₆H₁₀N₄

Average Mass

138.1704

Monoisotopic Mass

138.09054634

IUPAC Name

5-(aminomethyl)-2-methylpyrimidin-4-amine

Traditional Name

5-(aminomethyl)-2-methylpyrimidin-4-amine

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C6H10N4/c1-4-9-3-5(2-7)6(8)10-4/h3H,2,7H2,1H3,(H2,8,9,10)

InChI Key

OZOHTVFCSKFMLL-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as aralkylamines. These are alkylamines in which the alkyl group is substituted at one carbon atom by an aromatic hydrocarbyl group.

Kingdom

Organic compounds

Super Class

Organic nitrogen compounds

Class

Organonitrogen compounds

Sub Class

Amines

Direct Parent

Aralkylamines

Alternative Parents

Substituents

Aralkylamine
Imidolactam
Pyrimidine
Hydropyrimidine
Heteroaromatic compound
Azacycle
Organoheterocyclic compound
Organopnictogen compound
Hydrocarbon derivative
Primary amine
Primary aliphatic amine
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

aminopyrimidine (CHEBI:44549 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	19.5 g/L	ALOGPS
logP	-0.75	ALOGPS
logP	-0.47	ChemAxon
logS	-0.85	ALOGPS
pKa (Strongest Basic)	8.5	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	77.82 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	40.83 m³·mol⁻¹	ChemAxon
Polarizability	14.61 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 (Non-derivatized) - 70eV, Positive	splash10-0abi-4900000000-6a128bae64f060f3fc48	2017-08-28	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0079-0900000000-3babb20c7a3350e2dc4d	2017-07-26	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-00di-2900000000-04b87e55412c9a250cab	2017-07-26	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0fl1-9300000000-94fc934e6f7be9df4eaf	2017-07-26	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-000i-1900000000-a79eb04b4de93dc8ba44	2017-07-26	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-000i-4900000000-78a3ad804a8168a32785	2017-07-26	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9100000000-6900f4a506f5cb99dc48	2017-07-26	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	410.7
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-24	346.2
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (void)	2025-10-24	37.6
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-24	215.8
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-24	283.7
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (void)	2025-10-24	280.9
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	380.6
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	880.4
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-24	612.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	161.5
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	561.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	173.8
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	45.9
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	360.9
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	671.5
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	57.1
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	187.9
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-24	631.3
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-24	549.7

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	4-Amino-5-aminomethyl-2-methylpyrimidine_TMS_1	CC1=NC=C(CN[Si](C)(C)C)C(N)=N1	standard non polar	2025-10-24	2045.5
Gas Chromatography	4-Amino-5-aminomethyl-2-methylpyrimidine_TMS_2	CC1=NC=C(CN)C(N[Si](C)(C)C)=N1	standard non polar	2025-10-24	2325.18
Gas Chromatography	4-Amino-5-aminomethyl-2-methylpyrimidine_TMS_3	CC1=NC=C(CN[Si](C)(C)C)C(N[Si](C)(C)C)=N1	standard non polar	2025-10-24	1872.58
Gas Chromatography	4-Amino-5-aminomethyl-2-methylpyrimidine_TMS_4	CC1=NC=C(CN([Si](C)(C)C)[Si](C)(C)C)C(N)=N1	standard non polar	2025-10-24	1340.72
Gas Chromatography	4-Amino-5-aminomethyl-2-methylpyrimidine_TMS_5	CC1=NC=C(CN)C(N([Si](C)(C)C)[Si](C)(C)C)=N1	standard non polar	2025-10-24	1635.62
Gas Chromatography	4-Amino-5-aminomethyl-2-methylpyrimidine_TMS_6	CC1=NC=C(CN([Si](C)(C)C)[Si](C)(C)C)C(N[Si](C)(C)C)=N1	standard non polar	2025-10-24	1680.78
Gas Chromatography	4-Amino-5-aminomethyl-2-methylpyrimidine_TMS_7	CC1=NC=C(CN[Si](C)(C)C)C(N([Si](C)(C)C)[Si](C)(C)C)=N1	standard non polar	2025-10-24	1769.57
Gas Chromatography	4-Amino-5-aminomethyl-2-methylpyrimidine_TMS_8	CC1=NC=C(CN([Si](C)(C)C)[Si](C)(C)C)C(N([Si](C)(C)C)[Si](C)(C)C)=N1	standard non polar	2025-10-24	2180.1
Gas Chromatography	4-Amino-5-aminomethyl-2-methylpyrimidine_TMS_1	CC1=NC=C(CN[Si](C)(C)C)C(N)=N1	standard polar	2025-10-24	2098.21
Gas Chromatography	4-Amino-5-aminomethyl-2-methylpyrimidine_TMS_2	CC1=NC=C(CN)C(N[Si](C)(C)C)=N1	standard polar	2025-10-24	1972.22
Gas Chromatography	4-Amino-5-aminomethyl-2-methylpyrimidine_TMS_3	CC1=NC=C(CN[Si](C)(C)C)C(N[Si](C)(C)C)=N1	standard polar	2025-10-24	2014.54
Gas Chromatography	4-Amino-5-aminomethyl-2-methylpyrimidine_TMS_4	CC1=NC=C(CN([Si](C)(C)C)[Si](C)(C)C)C(N)=N1	standard polar	2025-10-24	2158.14
Gas Chromatography	4-Amino-5-aminomethyl-2-methylpyrimidine_TMS_5	CC1=NC=C(CN)C(N([Si](C)(C)C)[Si](C)(C)C)=N1	standard polar	2025-10-24	2464.1
Gas Chromatography	4-Amino-5-aminomethyl-2-methylpyrimidine_TMS_6	CC1=NC=C(CN([Si](C)(C)C)[Si](C)(C)C)C(N[Si](C)(C)C)=N1	standard polar	2025-10-24	1438.8
Gas Chromatography	4-Amino-5-aminomethyl-2-methylpyrimidine_TMS_7	CC1=NC=C(CN[Si](C)(C)C)C(N([Si](C)(C)C)[Si](C)(C)C)=N1	standard polar	2025-10-24	2310.55
Gas Chromatography	4-Amino-5-aminomethyl-2-methylpyrimidine_TMS_8	CC1=NC=C(CN([Si](C)(C)C)[Si](C)(C)C)C(N([Si](C)(C)C)[Si](C)(C)C)=N1	standard polar	2025-10-24	1868.95

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	16	Human feces; Human ; Cattle
Bacteria/Eubacteria	Proteobacteria	1	Human ; Human feces

Exposure Sources

Other Exposures

Source Type	Data Source	Reference
Drugs - Antimicrobial	U.S. Environmental Protection Agency	CompTox
Cosmetics	U.S. Environmental Protection Agency	CompTox
Domestics	U.S. Environmental Protection Agency	CompTox

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

DB03204

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

C20267

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

66762

PDB ID

Not Available

ChEBI ID

44549

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 4-Amino-5-aminomethyl-2-methylpyrimidine (MMDBc0051920)

MOL for #<Metabolite:0x00007f9ac7d21ec8>

3D MOL for #<Metabolite:0x00007f9ac7d21ec8>

3D SDF for #<Metabolite:0x00007f9ac7d21ec8>

3D-SDF for #<Metabolite:0x00007f9ac7d21ec8>

PDB for #<Metabolite:0x00007f9ac7d21ec8>

3D PDB for #<Metabolite:0x00007f9ac7d21ec8>

SMILES for #<Metabolite:0x00007f9ac7d21ec8>

INCHI for #<Metabolite:0x00007f9ac7d21ec8>

Structure for #<Metabolite:0x00007f9ac7d21ec8>

3D Structure for #<Metabolite:0x00007f9ac7d21ec8>