Record Information |
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Version | 5.0 |
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Status | Detected but not Quantified |
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Creation Date | 2021-09-11 11:42:52 UTC |
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Update Date | 2021-09-26 23:06:28 UTC |
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HMDB ID | HMDB0253320 |
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Secondary Accession Numbers | None |
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Metabolite Identification |
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Common Name | [(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate |
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Description | [3-azido-5-(4-hydroxy-5-methyl-2-oxo-1,2-dihydropyrimidin-1-yl)oxolan-2-yl]methyl 2-amino-3-methylpentanoate belongs to the class of organic compounds known as pyrimidine 2',3'-dideoxyribonucleosides. Pyrimidine 2',3'-dideoxyribonucleosides are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at positions 2 and 3. Based on a literature review a significant number of articles have been published on [3-azido-5-(4-hydroxy-5-methyl-2-oxo-1,2-dihydropyrimidin-1-yl)oxolan-2-yl]methyl 2-amino-3-methylpentanoate. This compound has been identified in human blood as reported by (PMID: 31557052 ). [(2s,3s,5r)-3-azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2s,3s)-2-amino-3-methylpentanoate is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically [(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources. |
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Structure | CCC(C)C(N)C(=O)OCC1OC(CC1N=[N+]=[N-])N1C=C(C)C(=O)NC1=O InChI=1S/C16H24N6O5/c1-4-8(2)13(17)15(24)26-7-11-10(20-21-18)5-12(27-11)22-6-9(3)14(23)19-16(22)25/h6,8,10-13H,4-5,7,17H2,1-3H3,(H,19,23,25) |
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Synonyms | Value | Source |
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[3-Azido-5-(4-hydroxy-5-methyl-2-oxo-1,2-dihydropyrimidin-1-yl)oxolan-2-yl]methyl 2-amino-3-methylpentanoic acid | Generator | [(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoic acid | Generator |
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Chemical Formula | C16H24N6O5 |
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Average Molecular Weight | 380.405 |
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Monoisotopic Molecular Weight | 380.180817897 |
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IUPAC Name | [3-azido-5-(5-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)oxolan-2-yl]methyl 2-amino-3-methylpentanoate |
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Traditional Name | [3-azido-5-(5-methyl-2,4-dioxo-3H-pyrimidin-1-yl)oxolan-2-yl]methyl 2-amino-3-methylpentanoate |
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CAS Registry Number | Not Available |
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SMILES | CCC(C)C(N)C(=O)OCC1OC(CC1N=[N+]=[N-])N1C=C(C)C(=O)NC1=O |
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InChI Identifier | InChI=1S/C16H24N6O5/c1-4-8(2)13(17)15(24)26-7-11-10(20-21-18)5-12(27-11)22-6-9(3)14(23)19-16(22)25/h6,8,10-13H,4-5,7,17H2,1-3H3,(H,19,23,25) |
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InChI Key | QUANSGVUESEHKX-UHFFFAOYSA-N |
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Chemical Taxonomy |
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Description | Belongs to the class of organic compounds known as pyrimidine 2',3'-dideoxyribonucleosides. Pyrimidine 2',3'-dideoxyribonucleosides are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at positions 2 and 3. |
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Kingdom | Organic compounds |
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Super Class | Nucleosides, nucleotides, and analogues |
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Class | Pyrimidine nucleosides |
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Sub Class | Pyrimidine 2',3'-dideoxyribonucleosides |
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Direct Parent | Pyrimidine 2',3'-dideoxyribonucleosides |
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Alternative Parents | |
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Substituents | - Pyrimidine 2',3'-dideoxyribonucleoside
- Isoleucine or derivatives
- Alpha-amino acid ester
- Alpha-amino acid or derivatives
- Fatty acid ester
- Pyrimidone
- Hydropyrimidine
- Fatty acyl
- Pyrimidine
- Heteroaromatic compound
- Oxolane
- Vinylogous amide
- Amino acid or derivatives
- Azo compound
- Azo imide
- Carboxylic acid ester
- Lactam
- Urea
- Oxacycle
- Organoheterocyclic compound
- Azacycle
- Monocarboxylic acid or derivatives
- Carboxylic acid derivative
- Organic zwitterion
- Hydrocarbon derivative
- Organic oxide
- Organic nitrogen compound
- Primary aliphatic amine
- Carbonyl group
- Amine
- Primary amine
- Organonitrogen compound
- Organooxygen compound
- Organic salt
- Organic oxygen compound
- Aromatic heteromonocyclic compound
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Molecular Framework | Aromatic heteromonocyclic compounds |
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External Descriptors | Not Available |
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Ontology |
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Physiological effect | Not Available |
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Disposition | |
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Process | Not Available |
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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 SectionsPredictor | Adduct Type | CCS Value (Å2) | Reference |
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DeepCCS | [M+H]+ | 193.707 | 30932474 | DeepCCS | [M-H]- | 191.349 | 30932474 | DeepCCS | [M-2H]- | 225.337 | 30932474 | DeepCCS | [M+Na]+ | 200.972 | 30932474 |
Predicted Kovats Retention IndicesUnderivatizedMetabolite | SMILES | Kovats RI Value | Column Type | Reference |
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[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate | CCC(C)C(N)C(=O)OCC1OC(CC1N=[N+]=[N-])N1C=C(C)C(=O)NC1=O | 4253.3 | Standard polar | 33892256 | [(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate | CCC(C)C(N)C(=O)OCC1OC(CC1N=[N+]=[N-])N1C=C(C)C(=O)NC1=O | 2685.6 | Standard non polar | 33892256 | [(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate | CCC(C)C(N)C(=O)OCC1OC(CC1N=[N+]=[N-])N1C=C(C)C(=O)NC1=O | 2951.4 | Semi standard non polar | 33892256 |
DerivatizedDerivative Name / Structure | SMILES | Kovats RI Value | Column Type | Reference |
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[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,1TMS,isomer #1 | CCC(C)C(N[Si](C)(C)C)C(=O)OCC1OC(N2C=C(C)C(=O)[NH]C2=O)CC1N=[N+]=[N-] | 3147.7 | Semi standard non polar | 33892256 | [(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,1TMS,isomer #1 | CCC(C)C(N[Si](C)(C)C)C(=O)OCC1OC(N2C=C(C)C(=O)[NH]C2=O)CC1N=[N+]=[N-] | 3070.0 | Standard non polar | 33892256 | [(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,1TMS,isomer #1 | CCC(C)C(N[Si](C)(C)C)C(=O)OCC1OC(N2C=C(C)C(=O)[NH]C2=O)CC1N=[N+]=[N-] | 4825.0 | Standard polar | 33892256 | [(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,1TMS,isomer #2 | CCC(C)C(N)C(=O)OCC1OC(N2C=C(C)C(=O)N([Si](C)(C)C)C2=O)CC1N=[N+]=[N-] | 3116.1 | Semi standard non polar | 33892256 | [(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,1TMS,isomer #2 | CCC(C)C(N)C(=O)OCC1OC(N2C=C(C)C(=O)N([Si](C)(C)C)C2=O)CC1N=[N+]=[N-] | 3127.1 | Standard non polar | 33892256 | [(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,1TMS,isomer #2 | CCC(C)C(N)C(=O)OCC1OC(N2C=C(C)C(=O)N([Si](C)(C)C)C2=O)CC1N=[N+]=[N-] | 5254.4 | Standard polar | 33892256 | [(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,2TMS,isomer #1 | CCC(C)C(C(=O)OCC1OC(N2C=C(C)C(=O)[NH]C2=O)CC1N=[N+]=[N-])N([Si](C)(C)C)[Si](C)(C)C | 3171.3 | Semi standard non polar | 33892256 | [(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,2TMS,isomer #1 | CCC(C)C(C(=O)OCC1OC(N2C=C(C)C(=O)[NH]C2=O)CC1N=[N+]=[N-])N([Si](C)(C)C)[Si](C)(C)C | 3195.4 | Standard non polar | 33892256 | [(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,2TMS,isomer #1 | CCC(C)C(C(=O)OCC1OC(N2C=C(C)C(=O)[NH]C2=O)CC1N=[N+]=[N-])N([Si](C)(C)C)[Si](C)(C)C | 4604.2 | Standard polar | 33892256 | [(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,2TMS,isomer #2 | CCC(C)C(N[Si](C)(C)C)C(=O)OCC1OC(N2C=C(C)C(=O)N([Si](C)(C)C)C2=O)CC1N=[N+]=[N-] | 3119.7 | Semi standard non polar | 33892256 | [(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,2TMS,isomer #2 | CCC(C)C(N[Si](C)(C)C)C(=O)OCC1OC(N2C=C(C)C(=O)N([Si](C)(C)C)C2=O)CC1N=[N+]=[N-] | 3110.8 | Standard non polar | 33892256 | [(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,2TMS,isomer #2 | CCC(C)C(N[Si](C)(C)C)C(=O)OCC1OC(N2C=C(C)C(=O)N([Si](C)(C)C)C2=O)CC1N=[N+]=[N-] | 4575.3 | Standard polar | 33892256 | [(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,3TMS,isomer #1 | CCC(C)C(C(=O)OCC1OC(N2C=C(C)C(=O)N([Si](C)(C)C)C2=O)CC1N=[N+]=[N-])N([Si](C)(C)C)[Si](C)(C)C | 3223.4 | Semi standard non polar | 33892256 | [(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,3TMS,isomer #1 | CCC(C)C(C(=O)OCC1OC(N2C=C(C)C(=O)N([Si](C)(C)C)C2=O)CC1N=[N+]=[N-])N([Si](C)(C)C)[Si](C)(C)C | 3227.1 | Standard non polar | 33892256 | [(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,3TMS,isomer #1 | CCC(C)C(C(=O)OCC1OC(N2C=C(C)C(=O)N([Si](C)(C)C)C2=O)CC1N=[N+]=[N-])N([Si](C)(C)C)[Si](C)(C)C | 4346.6 | Standard polar | 33892256 | [(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,1TBDMS,isomer #1 | CCC(C)C(N[Si](C)(C)C(C)(C)C)C(=O)OCC1OC(N2C=C(C)C(=O)[NH]C2=O)CC1N=[N+]=[N-] | 3370.4 | Semi standard non polar | 33892256 | [(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,1TBDMS,isomer #1 | CCC(C)C(N[Si](C)(C)C(C)(C)C)C(=O)OCC1OC(N2C=C(C)C(=O)[NH]C2=O)CC1N=[N+]=[N-] | 3290.1 | Standard non polar | 33892256 | [(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,1TBDMS,isomer #1 | CCC(C)C(N[Si](C)(C)C(C)(C)C)C(=O)OCC1OC(N2C=C(C)C(=O)[NH]C2=O)CC1N=[N+]=[N-] | 4820.3 | Standard polar | 33892256 | [(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,1TBDMS,isomer #2 | CCC(C)C(N)C(=O)OCC1OC(N2C=C(C)C(=O)N([Si](C)(C)C(C)(C)C)C2=O)CC1N=[N+]=[N-] | 3317.2 | Semi standard non polar | 33892256 | [(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,1TBDMS,isomer #2 | CCC(C)C(N)C(=O)OCC1OC(N2C=C(C)C(=O)N([Si](C)(C)C(C)(C)C)C2=O)CC1N=[N+]=[N-] | 3340.7 | Standard non polar | 33892256 | [(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,1TBDMS,isomer #2 | CCC(C)C(N)C(=O)OCC1OC(N2C=C(C)C(=O)N([Si](C)(C)C(C)(C)C)C2=O)CC1N=[N+]=[N-] | 5207.4 | Standard polar | 33892256 | [(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,2TBDMS,isomer #1 | CCC(C)C(C(=O)OCC1OC(N2C=C(C)C(=O)[NH]C2=O)CC1N=[N+]=[N-])N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C | 3632.6 | Semi standard non polar | 33892256 | [(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,2TBDMS,isomer #1 | CCC(C)C(C(=O)OCC1OC(N2C=C(C)C(=O)[NH]C2=O)CC1N=[N+]=[N-])N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C | 3568.9 | Standard non polar | 33892256 | [(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,2TBDMS,isomer #1 | CCC(C)C(C(=O)OCC1OC(N2C=C(C)C(=O)[NH]C2=O)CC1N=[N+]=[N-])N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C | 4573.6 | Standard polar | 33892256 | [(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,2TBDMS,isomer #2 | CCC(C)C(N[Si](C)(C)C(C)(C)C)C(=O)OCC1OC(N2C=C(C)C(=O)N([Si](C)(C)C(C)(C)C)C2=O)CC1N=[N+]=[N-] | 3556.0 | Semi standard non polar | 33892256 | [(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,2TBDMS,isomer #2 | CCC(C)C(N[Si](C)(C)C(C)(C)C)C(=O)OCC1OC(N2C=C(C)C(=O)N([Si](C)(C)C(C)(C)C)C2=O)CC1N=[N+]=[N-] | 3509.5 | Standard non polar | 33892256 | [(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,2TBDMS,isomer #2 | CCC(C)C(N[Si](C)(C)C(C)(C)C)C(=O)OCC1OC(N2C=C(C)C(=O)N([Si](C)(C)C(C)(C)C)C2=O)CC1N=[N+]=[N-] | 4534.4 | Standard polar | 33892256 | [(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,3TBDMS,isomer #1 | CCC(C)C(C(=O)OCC1OC(N2C=C(C)C(=O)N([Si](C)(C)C(C)(C)C)C2=O)CC1N=[N+]=[N-])N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C | 3860.9 | Semi standard non polar | 33892256 | [(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,3TBDMS,isomer #1 | CCC(C)C(C(=O)OCC1OC(N2C=C(C)C(=O)N([Si](C)(C)C(C)(C)C)C2=O)CC1N=[N+]=[N-])N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C | 3757.2 | Standard non polar | 33892256 | [(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,3TBDMS,isomer #1 | CCC(C)C(C(=O)OCC1OC(N2C=C(C)C(=O)N([Si](C)(C)C(C)(C)C)C2=O)CC1N=[N+]=[N-])N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C | 4327.8 | Standard polar | 33892256 |
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