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MedKoo Cat#: 145419 | Name: Agmatidine

Description:

WARNING: This product is for research use only, not for human or veterinary use.

Agmatidine is purposeful in that it shows that bacteria and archaea have developed very similar strategies for reading the isoleucine codon AUA while discriminating against the methionine codon AUG.

Chemical Structure

Agmatidine
Agmatidine
CAS#1221169-70-5

Theoretical Analysis

MedKoo Cat#: 145419

Name: Agmatidine

CAS#: 1221169-70-5

Chemical Formula: C14H25N7O4

Exact Mass: 355.1968

Molecular Weight: 355.40

Elemental Analysis: C, 47.31; H, 7.09; N, 27.59; O, 18.01

Price and Availability

This product is currently not in stock but may be available through custom synthesis. To ensure cost efficiency, the minimum order quantity is 1 gram. The estimated lead time is 2 to 4 months, with pricing dependent on the complexity of the synthesis (typically high for intricate chemistries). Quotes for quantities below 1 gram will not be provided. To request a quote, please click the button below. Note: If this product becomes available in stock in the future, pricing will be listed accordingly.
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Related CAS #
No Data
Synonym
Agmatidine; 2-AGMATINYLCYTIDINE;
IUPAC/Chemical Name
1-(4-(((E)-4-amino-1-((2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl)pyrimidin-2(1H)-ylidene)amino)butyl)guanidine
InChi Key
NHQSDCRALZPVAJ-HJQYOEGKSA-N
InChi Code
1S/C14H25N7O4/c15-9-3-6-21(12-11(24)10(23)8(7-22)25-12)14(20-9)19-5-2-1-4-18-13(16)17/h3,6,8,10-12,22-24H,1-2,4-5,7H2,(H2,15,19,20)(H4,16,17,18)/t8-,10-,11-,12-/m1/s1
SMILES Code
NC(=N)NCCCC\N=C1/N=C(N)C=CN1[C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O
Appearance
To be determined
Purity
>98% (or refer to the Certificate of Analysis)
Shipping Condition
Shipped under ambient temperature as non-hazardous chemical. This product is stable enough for a few weeks during ordinary shipping and time spent in Customs.
Storage Condition
Dry, dark and at 0 -4 C for short term (days to weeks) or -20 C for long term(months to years).
Solubility
To be determined
Shelf Life
>2 years if stored properly
Drug Formulation
To be determined
Stock Solution Storage
0 - 4 C for short term (days to weeks), or -20 C for long term (months).
HS Tariff Code
2934.99.9001
More Info

Preparing Stock Solutions

The following data is based on the product molecular weight 355.40 Batch specific molecular weights may vary from batch to batch due to the degree of hydration, which will affect the solvent volumes required to prepare stock solutions.

Recalculate based on batch purity %
Concentration / Solvent Volume / Mass 1 mg 5 mg 10 mg
1 mM 1.15 mL 5.76 mL 11.51 mL
5 mM 0.23 mL 1.15 mL 2.3 mL
10 mM 0.12 mL 0.58 mL 1.15 mL
50 mM 0.02 mL 0.12 mL 0.23 mL
1: Mandal D, Köhrer C, Su D, Russell SP, Krivos K, Castleberry CM, Blum P, Limbach PA, Söll D, RajBhandary UL. Agmatidine, a modified cytidine in the anticodon of archaeal tRNA(Ile), base pairs with adenosine but not with guanosine. Proc Natl Acad Sci U S A. 2010 Feb 16;107(7):2872-7. doi: 10.1073/pnas.0914869107. Epub 2010 Jan 26. PMID: 20133752; PMCID: PMC2840323. 2: Kopina BJ, Lauhon CT. Efficient preparation of 2,4-diaminopyrimidine nucleosides: total synthesis of lysidine and agmatidine. Org Lett. 2012 Aug 17;14(16):4118-21. doi: 10.1021/ol301769j. Epub 2012 Jul 30. PMID: 22845013. 3: Akiyama N, Ishiguro K, Yokoyama T, Miyauchi K, Nagao A, Shirouzu M, Suzuki T. Structural insights into the decoding capability of isoleucine tRNAs with lysidine and agmatidine. Nat Struct Mol Biol. 2024 May;31(5):817-825. doi: 10.1038/s41594-024-01238-1. Epub 2024 Mar 27. PMID: 38538915. 4: Suzuki T, Numata T. Convergent evolution of AUA decoding in bacteria and archaea. RNA Biol. 2014;11(12):1586-96. doi: 10.4161/15476286.2014.992281. PMID: 25629511; PMCID: PMC4615378. 5: Phillips G, de Crécy-Lagard V. Biosynthesis and function of tRNA modifications in Archaea. Curr Opin Microbiol. 2011 Jun;14(3):335-41. doi: 10.1016/j.mib.2011.03.001. Epub 2011 Apr 4. PMID: 21470902. 6: Numata T. Mechanisms of the tRNA wobble cytidine modification essential for AUA codon decoding in prokaryotes. Biosci Biotechnol Biochem. 2015;79(3):347-53. doi: 10.1080/09168451.2014.975185. Epub 2014 Oct 28. PMID: 25348586. 7: Cantara WA, Crain PF, Rozenski J, McCloskey JA, Harris KA, Zhang X, Vendeix FA, Fabris D, Agris PF. The RNA Modification Database, RNAMDB: 2011 update. Nucleic Acids Res. 2011 Jan;39(Database issue):D195-201. doi: 10.1093/nar/gkq1028. Epub 2010 Nov 10. PMID: 21071406; PMCID: PMC3013656. 8: Dong J, Li F, Gao F, Wei J, Lin Y, Zhang Y, Lou J, Liu G, Dong Y, Liu L, Liu H, Wang J, Gong W. Structure of tRNA-Modifying Enzyme TiaS and Motions of Its Substrate Binding Zinc Ribbon. J Mol Biol. 2018 Oct 19;430(21):4183-4194. doi: 10.1016/j.jmb.2018.08.015. Epub 2018 Aug 16. PMID: 30121296. 9: Li F, Dong J, Hu X, Gong W, Li J, Shen J, Tian H, Wang J. A covalent approach for site-specific RNA labeling in Mammalian cells. Angew Chem Int Ed Engl. 2015 Apr 7;54(15):4597-602. doi: 10.1002/anie.201410433. Epub 2015 Feb 18. PMID: 25694369. 10: Voorhees RM, Mandal D, Neubauer C, Köhrer C, RajBhandary UL, Ramakrishnan V. The structural basis for specific decoding of AUA by isoleucine tRNA on the ribosome. Nat Struct Mol Biol. 2013 May;20(5):641-3. doi: 10.1038/nsmb.2545. Epub 2013 Mar 31. PMID: 23542153; PMCID: PMC3672977. 11: Osawa T, Kimura S, Terasaka N, Inanaga H, Suzuki T, Numata T. Structural basis of tRNA agmatinylation essential for AUA codon decoding. Nat Struct Mol Biol. 2011 Oct 16;18(11):1275-80. doi: 10.1038/nsmb.2144. PMID: 22002223. 12: Terasaka N, Kimura S, Osawa T, Numata T, Suzuki T. Biogenesis of 2-agmatinylcytidine catalyzed by the dual protein and RNA kinase TiaS. Nat Struct Mol Biol. 2011 Oct 16;18(11):1268-74. doi: 10.1038/nsmb.2121. PMID: 22002222. 13: Law KP, He W, Tao J, Zhang C. Characterization of the Exometabolome of Nitrosopumilus maritimus SCM1 by Liquid Chromatography-Ion Mobility Mass Spectrometry. Front Microbiol. 2021 Jul 1;12:658781. doi: 10.3389/fmicb.2021.658781. PMID: 34276593; PMCID: PMC8281238. 14: Ikeuchi Y, Kimura S, Numata T, Nakamura D, Yokogawa T, Ogata T, Wada T, Suzuki T, Suzuki T. Agmatine-conjugated cytidine in a tRNA anticodon is essential for AUA decoding in archaea. Nat Chem Biol. 2010 Apr;6(4):277-82. doi: 10.1038/nchembio.323. Epub 2010 Feb 7. PMID: 20139989. 15: Köhrer C, Mandal D, Gaston KW, Grosjean H, Limbach PA, Rajbhandary UL. Life without tRNAIle-lysidine synthetase: translation of the isoleucine codon AUA in Bacillus subtilis lacking the canonical tRNA2Ile. Nucleic Acids Res. 2014 Feb;42(3):1904-15. doi: 10.1093/nar/gkt1009. Epub 2013 Nov 4. PMID: 24194599; PMCID: PMC3919564. 16: Satpati P, Bauer P, Aqvist J. Energetic tuning by tRNA modifications ensures correct decoding of isoleucine and methionine on the ribosome. Chemistry. 2014 Aug 11;20(33):10271-5. doi: 10.1002/chem.201404016. Epub 2014 Jul 17. PMID: 25043149. 17: Di Giulio M. LUCA as well as the ancestors of archaea, bacteria and eukaryotes were progenotes: Inference from the distribution and diversity of the reading mechanism of the AUA and AUG codons in the domains of life. Biosystems. 2020 Dec;198:104239. doi: 10.1016/j.biosystems.2020.104239. Epub 2020 Sep 9. PMID: 32919036. 18: Numata T. [Molecular basis for tRNA(Ile) agmatinylation essential for AUA codon decoding]. Seikagaku. 2012 Dec;84(12):1004-8. Japanese. PMID: 23350510. 19: Hendrickson TL. The genetic code: an archaeal path to literacy. Nat Chem Biol. 2010 Apr;6(4):248-9. doi: 10.1038/nchembio.335. PMID: 20300092.