| Record Information |
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| Version | 5.0 |
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| Status | Expected but not Quantified |
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| Creation Date | 2021-09-24 07:43:57 UTC |
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| Update Date | 2021-09-24 07:43:57 UTC |
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| HMDB ID | HMDB0304168 |
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| Secondary Accession Numbers | None |
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| Metabolite Identification |
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| Common Name | 4-amino-2-methyl-5-diphosphomethylpyrimidine |
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| Description | 2-methyl-4-amino-5-hydroxymethylpyrimidine diphosphate, also known as hmp-pp or 4-amino-5-hydroxymethyl-2-methylpyrimidine-pp, is a member of the class of compounds known as organic pyrophosphates. Organic pyrophosphates are organic compounds containing the pyrophosphate oxoanion, with the structure OP([O-])(=O)OP(O)([O-])=O. 2-methyl-4-amino-5-hydroxymethylpyrimidine diphosphate is soluble (in water) and a moderately acidic compound (based on its pKa). 2-methyl-4-amino-5-hydroxymethylpyrimidine diphosphate can be found in a number of food items such as purple laver, japanese pumpkin, parsnip, and cloves, which makes 2-methyl-4-amino-5-hydroxymethylpyrimidine diphosphate a potential biomarker for the consumption of these food products. 2-methyl-4-amino-5-hydroxymethylpyrimidine diphosphate may be a unique E.coli metabolite. |
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| Structure | CC1=NC=C(COP([O-])(=O)OP([O-])([O-])=O)C(=N)N1 InChI=1S/C6H11N3O7P2/c1-4-8-2-5(6(7)9-4)3-15-18(13,14)16-17(10,11)12/h2H,3H2,1H3,(H,13,14)(H2,7,8,9)(H2,10,11,12)/p-3 |
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| Synonyms | | Value | Source |
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| 4-Amino-2-methyl-5-(diphosphooxymethyl)pyrimidine | ChEBI | | 4-Amino-2-methyl-5-diphosphonatooxymethylpyrimidine trianion | ChEBI | | 4-amino-2-Methyl-5-(diphosphonooxymethyl)pyrimidine | ChEBI |
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| Chemical Formula | C6H8N3O7P2 |
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| Average Molecular Weight | 296.093 |
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| Monoisotopic Molecular Weight | 295.985394345 |
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| IUPAC Name | {[(6-imino-2-methyl-1,6-dihydropyrimidin-5-yl)methyl phosphonato]oxy}phosphonate |
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| Traditional Name | [(4-imino-2-methyl-3H-pyrimidin-5-yl)methyl phosphonato]oxyphosphonate |
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| CAS Registry Number | Not Available |
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| SMILES | CC1=NC=C(COP([O-])(=O)OP([O-])([O-])=O)C(=N)N1 |
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| InChI Identifier | InChI=1S/C6H11N3O7P2/c1-4-8-2-5(6(7)9-4)3-15-18(13,14)16-17(10,11)12/h2H,3H2,1H3,(H,13,14)(H2,7,8,9)(H2,10,11,12)/p-3 |
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| InChI Key | AGQJQCFEPUVXNK-UHFFFAOYSA-K |
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| Chemical Taxonomy |
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| Description | Belongs to the class of organic compounds known as organic pyrophosphates. These are organic compounds containing the pyrophosphate oxoanion, with the structure OP([O-])(=O)OP(O)([O-])=O. |
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| Kingdom | Organic compounds |
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| Super Class | Organic oxygen compounds |
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| Class | Organic oxoanionic compounds |
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| Sub Class | Organic pyrophosphates |
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| Direct Parent | Organic pyrophosphates |
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| Alternative Parents | |
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| Substituents | - Organic pyrophosphate
- Aminopyrimidine
- Organic phosphoric acid derivative
- Phosphoric acid ester
- Pyrimidine
- Alkyl phosphate
- Imidolactam
- Heteroaromatic compound
- Azacycle
- Organoheterocyclic compound
- Amine
- Primary amine
- Hydrocarbon derivative
- Organooxygen compound
- Organonitrogen compound
- Organic oxide
- Organopnictogen compound
- Organic nitrogen compound
- Organic anion
- Aromatic heteromonocyclic compound
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| Molecular Framework | Aromatic heteromonocyclic compounds |
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| External Descriptors | |
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| Ontology |
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| Physiological effect | Not Available |
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| Disposition | |
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| Process | |
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| Role | Not Available |
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| Physical Properties |
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| State | Not Available |
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| Experimental Molecular Properties | | Property | Value | Reference |
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| Melting Point | Not Available | Not Available | | Boiling Point | Not Available | Not Available | | Water Solubility | Not Available | Not Available | | LogP | Not Available | Not Available |
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| Experimental Chromatographic Properties | Not Available |
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| Predicted Molecular Properties | |
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| Predicted Chromatographic Properties | Predicted Collision Cross SectionsPredicted Retention Times Underivatized| Chromatographic Method | Retention Time | Reference |
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| Predicted by Siyang on May 30, 2022 | 9.7329 minutes | 33406817 | | Predicted by Siyang using ReTip algorithm on June 8, 2022 | 8.17 minutes | 32390414 | | Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid | 787.8 seconds | 40023050 | | Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid | 267.3 seconds | 40023050 | | Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid | 73.0 seconds | 40023050 | | Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid | 159.6 seconds | 40023050 | | RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid | 49.3 seconds | 40023050 | | Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid | 253.0 seconds | 40023050 | | BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid | 285.5 seconds | 40023050 | | HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate) | 730.6 seconds | 40023050 | | UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid | 623.1 seconds | 40023050 | | BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid | 66.3 seconds | 40023050 | | UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid | 1011.8 seconds | 40023050 | | SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid | 207.7 seconds | 40023050 | | RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid | 169.1 seconds | 40023050 | | MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate | 568.8 seconds | 40023050 | | KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA | 371.7 seconds | 40023050 | | Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water | 495.7 seconds | 40023050 |
Predicted Kovats Retention IndicesDerivatized| Derivative Name / Structure | SMILES | Kovats RI Value | Column Type | Reference |
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| 4-amino-2-methyl-5-diphosphomethylpyrimidine,1TMS,isomer #1 | CC1=NC=C(COP(=O)([O-])OP(=O)([O-])[O-])C(=N[Si](C)(C)C)[NH]1 | 2130.7 | Semi standard non polar | 33892256 | | 4-amino-2-methyl-5-diphosphomethylpyrimidine,1TMS,isomer #1 | CC1=NC=C(COP(=O)([O-])OP(=O)([O-])[O-])C(=N[Si](C)(C)C)[NH]1 | 2246.1 | Standard non polar | 33892256 | | 4-amino-2-methyl-5-diphosphomethylpyrimidine,1TMS,isomer #1 | CC1=NC=C(COP(=O)([O-])OP(=O)([O-])[O-])C(=N[Si](C)(C)C)[NH]1 | 3323.1 | Standard polar | 33892256 | | 4-amino-2-methyl-5-diphosphomethylpyrimidine,1TMS,isomer #2 | CC1=NC=C(COP(=O)([O-])OP(=O)([O-])[O-])C(=N)N1[Si](C)(C)C | 2305.4 | Semi standard non polar | 33892256 | | 4-amino-2-methyl-5-diphosphomethylpyrimidine,1TMS,isomer #2 | CC1=NC=C(COP(=O)([O-])OP(=O)([O-])[O-])C(=N)N1[Si](C)(C)C | 2283.1 | Standard non polar | 33892256 | | 4-amino-2-methyl-5-diphosphomethylpyrimidine,1TMS,isomer #2 | CC1=NC=C(COP(=O)([O-])OP(=O)([O-])[O-])C(=N)N1[Si](C)(C)C | 3423.9 | Standard polar | 33892256 | | 4-amino-2-methyl-5-diphosphomethylpyrimidine,2TMS,isomer #1 | CC1=NC=C(COP(=O)([O-])OP(=O)([O-])[O-])C(=N[Si](C)(C)C)N1[Si](C)(C)C | 2285.5 | Semi standard non polar | 33892256 | | 4-amino-2-methyl-5-diphosphomethylpyrimidine,2TMS,isomer #1 | CC1=NC=C(COP(=O)([O-])OP(=O)([O-])[O-])C(=N[Si](C)(C)C)N1[Si](C)(C)C | 2351.9 | Standard non polar | 33892256 | | 4-amino-2-methyl-5-diphosphomethylpyrimidine,2TMS,isomer #1 | CC1=NC=C(COP(=O)([O-])OP(=O)([O-])[O-])C(=N[Si](C)(C)C)N1[Si](C)(C)C | 3051.3 | Standard polar | 33892256 | | 4-amino-2-methyl-5-diphosphomethylpyrimidine,1TBDMS,isomer #1 | CC1=NC=C(COP(=O)([O-])OP(=O)([O-])[O-])C(=N[Si](C)(C)C(C)(C)C)[NH]1 | 2384.8 | Semi standard non polar | 33892256 | | 4-amino-2-methyl-5-diphosphomethylpyrimidine,1TBDMS,isomer #1 | CC1=NC=C(COP(=O)([O-])OP(=O)([O-])[O-])C(=N[Si](C)(C)C(C)(C)C)[NH]1 | 2406.0 | Standard non polar | 33892256 | | 4-amino-2-methyl-5-diphosphomethylpyrimidine,1TBDMS,isomer #1 | CC1=NC=C(COP(=O)([O-])OP(=O)([O-])[O-])C(=N[Si](C)(C)C(C)(C)C)[NH]1 | 3347.4 | Standard polar | 33892256 | | 4-amino-2-methyl-5-diphosphomethylpyrimidine,1TBDMS,isomer #2 | CC1=NC=C(COP(=O)([O-])OP(=O)([O-])[O-])C(=N)N1[Si](C)(C)C(C)(C)C | 2536.3 | Semi standard non polar | 33892256 | | 4-amino-2-methyl-5-diphosphomethylpyrimidine,1TBDMS,isomer #2 | CC1=NC=C(COP(=O)([O-])OP(=O)([O-])[O-])C(=N)N1[Si](C)(C)C(C)(C)C | 2475.5 | Standard non polar | 33892256 | | 4-amino-2-methyl-5-diphosphomethylpyrimidine,1TBDMS,isomer #2 | CC1=NC=C(COP(=O)([O-])OP(=O)([O-])[O-])C(=N)N1[Si](C)(C)C(C)(C)C | 3341.7 | Standard polar | 33892256 | | 4-amino-2-methyl-5-diphosphomethylpyrimidine,2TBDMS,isomer #1 | CC1=NC=C(COP(=O)([O-])OP(=O)([O-])[O-])C(=N[Si](C)(C)C(C)(C)C)N1[Si](C)(C)C(C)(C)C | 2732.1 | Semi standard non polar | 33892256 | | 4-amino-2-methyl-5-diphosphomethylpyrimidine,2TBDMS,isomer #1 | CC1=NC=C(COP(=O)([O-])OP(=O)([O-])[O-])C(=N[Si](C)(C)C(C)(C)C)N1[Si](C)(C)C(C)(C)C | 2708.9 | Standard non polar | 33892256 | | 4-amino-2-methyl-5-diphosphomethylpyrimidine,2TBDMS,isomer #1 | CC1=NC=C(COP(=O)([O-])OP(=O)([O-])[O-])C(=N[Si](C)(C)C(C)(C)C)N1[Si](C)(C)C(C)(C)C | 3145.8 | Standard polar | 33892256 |
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| NMR Spectra| Spectrum Type | Description | Deposition Date | Source | View |
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| Predicted 1D NMR | 13C NMR Spectrum (1D, 100 MHz, H2O, predicted) | 2022-08-20 | Wishart Lab | View Spectrum | | Predicted 1D NMR | 1H NMR Spectrum (1D, 100 MHz, H2O, predicted) | 2022-08-20 | Wishart Lab | View Spectrum | | Predicted 1D NMR | 13C NMR Spectrum (1D, 1000 MHz, H2O, predicted) | 2022-08-20 | Wishart Lab | View Spectrum | | Predicted 1D NMR | 1H NMR Spectrum (1D, 1000 MHz, H2O, predicted) | 2022-08-20 | Wishart Lab | View Spectrum | | Predicted 1D NMR | 13C NMR Spectrum (1D, 200 MHz, H2O, predicted) | 2022-08-20 | Wishart Lab | View Spectrum | | Predicted 1D NMR | 1H NMR Spectrum (1D, 200 MHz, H2O, predicted) | 2022-08-20 | Wishart Lab | View Spectrum | | Predicted 1D NMR | 13C NMR Spectrum (1D, 300 MHz, H2O, predicted) | 2022-08-20 | Wishart Lab | View Spectrum | | Predicted 1D NMR | 1H NMR Spectrum (1D, 300 MHz, H2O, predicted) | 2022-08-20 | Wishart Lab | View Spectrum | | Predicted 1D NMR | 13C NMR Spectrum (1D, 400 MHz, H2O, predicted) | 2022-08-20 | Wishart Lab | View Spectrum | | Predicted 1D NMR | 1H NMR Spectrum (1D, 400 MHz, H2O, predicted) | 2022-08-20 | Wishart Lab | View Spectrum | | Predicted 1D NMR | 13C NMR Spectrum (1D, 500 MHz, H2O, predicted) | 2022-08-20 | Wishart Lab | View Spectrum | | Predicted 1D NMR | 1H NMR Spectrum (1D, 500 MHz, H2O, predicted) | 2022-08-20 | Wishart Lab | View Spectrum | | Predicted 1D NMR | 13C NMR Spectrum (1D, 600 MHz, H2O, predicted) | 2022-08-20 | Wishart Lab | View Spectrum | | Predicted 1D NMR | 1H NMR Spectrum (1D, 600 MHz, H2O, predicted) | 2022-08-20 | Wishart Lab | View Spectrum | | Predicted 1D NMR | 13C NMR Spectrum (1D, 700 MHz, H2O, predicted) | 2022-08-20 | Wishart Lab | View Spectrum | | Predicted 1D NMR | 1H NMR Spectrum (1D, 700 MHz, H2O, predicted) | 2022-08-20 | Wishart Lab | View Spectrum | | Predicted 1D NMR | 13C NMR Spectrum (1D, 800 MHz, H2O, predicted) | 2022-08-20 | Wishart Lab | View Spectrum | | Predicted 1D NMR | 1H NMR Spectrum (1D, 800 MHz, H2O, predicted) | 2022-08-20 | Wishart Lab | View Spectrum | | Predicted 1D NMR | 13C NMR Spectrum (1D, 900 MHz, H2O, predicted) | 2022-08-20 | Wishart Lab | View Spectrum | | Predicted 1D NMR | 1H NMR Spectrum (1D, 900 MHz, H2O, predicted) | 2022-08-20 | Wishart Lab | View Spectrum |
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