| Record Information |
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| Version | 5.0 |
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| Status | Expected but not Quantified |
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| Creation Date | 2013-05-09 20:57:09 UTC |
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| Update Date | 2022-03-07 03:17:39 UTC |
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| HMDB ID | HMDB0060133 |
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| Secondary Accession Numbers | |
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| Metabolite Identification |
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| Common Name | (24R)-24,25-Dihydroxycalciol |
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| Description | (24R)-24,25-Dihydroxycalciol belongs to the class of organic compounds known as vitamin d and derivatives. Vitamin D and derivatives are compounds containing a secosteroid backbone, usually secoergostane or secocholestane (24R)-24,25-Dihydroxycalciol is an extremely weak basic (essentially neutral) compound (based on its pKa). |
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| Structure | C[C@H](CC[C@@H](O)C(C)(C)O)[C@H]1CC[C@H]2\C(CCC[C@]12C)=C\C=C1/C[C@@H](O)CCC1=C InChI=1S/C27H44O3/c1-18-8-12-22(28)17-21(18)11-10-20-7-6-16-27(5)23(13-14-24(20)27)19(2)9-15-25(29)26(3,4)30/h10-11,19,22-25,28-30H,1,6-9,12-17H2,2-5H3/b20-10+,21-11+/t19-,22+,23-,24+,25-,27-/m1/s1 |
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| Synonyms | Not Available |
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| Chemical Formula | C27H44O3 |
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| Average Molecular Weight | 416.6365 |
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| Monoisotopic Molecular Weight | 416.329045274 |
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| IUPAC Name | (3R,6R)-6-[(1R,3aS,4E,7aR)-4-{2-[(1E,5S)-5-hydroxy-2-methylidenecyclohexylidene]ethylidene}-7a-methyl-octahydro-1H-inden-1-yl]-2-methylheptane-2,3-diol |
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| Traditional Name | (3R,6R)-6-[(1R,3aS,4E,7aR)-4-{2-[(1E,5S)-5-hydroxy-2-methylidenecyclohexylidene]ethylidene}-7a-methyl-hexahydro-1H-inden-1-yl]-2-methylheptane-2,3-diol |
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| CAS Registry Number | Not Available |
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| SMILES | C[C@H](CC[C@@H](O)C(C)(C)O)[C@H]1CC[C@H]2\C(CCC[C@]12C)=C\C=C1/C[C@@H](O)CCC1=C |
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| InChI Identifier | InChI=1S/C27H44O3/c1-18-8-12-22(28)17-21(18)11-10-20-7-6-16-27(5)23(13-14-24(20)27)19(2)9-15-25(29)26(3,4)30/h10-11,19,22-25,28-30H,1,6-9,12-17H2,2-5H3/b20-10+,21-11+/t19-,22+,23-,24+,25-,27-/m1/s1 |
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| InChI Key | FCKJYANJHNLEEP-QJQBGXGLSA-N |
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| Chemical Taxonomy |
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| Description | Belongs to the class of organic compounds known as vitamin d and derivatives. Vitamin D and derivatives are compounds containing a secosteroid backbone, usually secoergostane or secocholestane. |
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| Kingdom | Organic compounds |
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| Super Class | Lipids and lipid-like molecules |
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| Class | Steroids and steroid derivatives |
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| Sub Class | Vitamin D and derivatives |
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| Direct Parent | Vitamin D and derivatives |
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| Alternative Parents | |
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| Substituents | - Triterpenoid
- Tertiary alcohol
- Cyclic alcohol
- Secondary alcohol
- Organic oxygen compound
- Hydrocarbon derivative
- Organooxygen compound
- Alcohol
- Aliphatic homopolycyclic compound
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| Molecular Framework | Aliphatic homopolycyclic 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 SectionsPredicted Retention Times Underivatized| Chromatographic Method | Retention Time | Reference |
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| Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm √ó 2.1 mm; 1.7 Œºmparticle diameter). Predicted by Afia on May 17, 2022. | 8.41 minutes | 32390414 | | Predicted by Siyang on May 30, 2022 | 20.0883 minutes | 33406817 | | Predicted by Siyang using ReTip algorithm on June 8, 2022 | 1.24 minutes | 32390414 | | Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid | 3208.0 seconds | 40023050 | | Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid | 414.4 seconds | 40023050 | | Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid | 244.5 seconds | 40023050 | | Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid | 188.7 seconds | 40023050 | | RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid | 506.9 seconds | 40023050 | | Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid | 948.2 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 | 894.0 seconds | 40023050 | | HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate) | 94.7 seconds | 40023050 | | UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid | 1681.8 seconds | 40023050 | | BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid | 603.1 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 | 1753.7 seconds | 40023050 | | SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid | 604.9 seconds | 40023050 | | RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid | 528.2 seconds | 40023050 | | MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate | 268.0 seconds | 40023050 | | KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA | 554.6 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 | 8.7 seconds | 40023050 |
Predicted Kovats Retention IndicesUnderivatizedDerivatized| Derivative Name / Structure | SMILES | Kovats RI Value | Column Type | Reference |
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| (24R)-24,25-Dihydroxycalciol,1TMS,isomer #1 | C=C1CC[C@H](O)C/C1=C\C=C1/CCC[C@@]2(C)[C@H]1CC[C@@H]2[C@H](C)CC[C@@H](O[Si](C)(C)C)C(C)(C)O | 3482.0 | Semi standard non polar | 33892256 | | (24R)-24,25-Dihydroxycalciol,1TMS,isomer #2 | C=C1CC[C@H](O)C/C1=C\C=C1/CCC[C@@]2(C)[C@H]1CC[C@@H]2[C@H](C)CC[C@@H](O)C(C)(C)O[Si](C)(C)C | 3515.6 | Semi standard non polar | 33892256 | | (24R)-24,25-Dihydroxycalciol,1TMS,isomer #3 | C=C1CC[C@H](O[Si](C)(C)C)C/C1=C\C=C1/CCC[C@@]2(C)[C@H]1CC[C@@H]2[C@H](C)CC[C@@H](O)C(C)(C)O | 3434.0 | Semi standard non polar | 33892256 | | (24R)-24,25-Dihydroxycalciol,2TMS,isomer #1 | C=C1CC[C@H](O[Si](C)(C)C)C/C1=C\C=C1/CCC[C@@]2(C)[C@H]1CC[C@@H]2[C@H](C)CC[C@@H](O[Si](C)(C)C)C(C)(C)O | 3435.4 | Semi standard non polar | 33892256 | | (24R)-24,25-Dihydroxycalciol,2TMS,isomer #2 | C=C1CC[C@H](O)C/C1=C\C=C1/CCC[C@@]2(C)[C@H]1CC[C@@H]2[C@H](C)CC[C@@H](O[Si](C)(C)C)C(C)(C)O[Si](C)(C)C | 3532.1 | Semi standard non polar | 33892256 | | (24R)-24,25-Dihydroxycalciol,2TMS,isomer #3 | C=C1CC[C@H](O[Si](C)(C)C)C/C1=C\C=C1/CCC[C@@]2(C)[C@H]1CC[C@@H]2[C@H](C)CC[C@@H](O)C(C)(C)O[Si](C)(C)C | 3486.0 | Semi standard non polar | 33892256 | | (24R)-24,25-Dihydroxycalciol,3TMS,isomer #1 | C=C1CC[C@H](O[Si](C)(C)C)C/C1=C\C=C1/CCC[C@@]2(C)[C@H]1CC[C@@H]2[C@H](C)CC[C@@H](O[Si](C)(C)C)C(C)(C)O[Si](C)(C)C | 3503.3 | Semi standard non polar | 33892256 | | (24R)-24,25-Dihydroxycalciol,1TBDMS,isomer #1 | C=C1CC[C@H](O)C/C1=C\C=C1/CCC[C@@]2(C)[C@H]1CC[C@@H]2[C@H](C)CC[C@@H](O[Si](C)(C)C(C)(C)C)C(C)(C)O | 3709.8 | Semi standard non polar | 33892256 | | (24R)-24,25-Dihydroxycalciol,1TBDMS,isomer #2 | C=C1CC[C@H](O)C/C1=C\C=C1/CCC[C@@]2(C)[C@H]1CC[C@@H]2[C@H](C)CC[C@@H](O)C(C)(C)O[Si](C)(C)C(C)(C)C | 3741.1 | Semi standard non polar | 33892256 | | (24R)-24,25-Dihydroxycalciol,1TBDMS,isomer #3 | C=C1CC[C@H](O[Si](C)(C)C(C)(C)C)C/C1=C\C=C1/CCC[C@@]2(C)[C@H]1CC[C@@H]2[C@H](C)CC[C@@H](O)C(C)(C)O | 3629.6 | Semi standard non polar | 33892256 | | (24R)-24,25-Dihydroxycalciol,2TBDMS,isomer #1 | C=C1CC[C@H](O[Si](C)(C)C(C)(C)C)C/C1=C\C=C1/CCC[C@@]2(C)[C@H]1CC[C@@H]2[C@H](C)CC[C@@H](O[Si](C)(C)C(C)(C)C)C(C)(C)O | 3877.9 | Semi standard non polar | 33892256 | | (24R)-24,25-Dihydroxycalciol,2TBDMS,isomer #2 | C=C1CC[C@H](O)C/C1=C\C=C1/CCC[C@@]2(C)[C@H]1CC[C@@H]2[C@H](C)CC[C@@H](O[Si](C)(C)C(C)(C)C)C(C)(C)O[Si](C)(C)C(C)(C)C | 3984.1 | Semi standard non polar | 33892256 | | (24R)-24,25-Dihydroxycalciol,2TBDMS,isomer #3 | C=C1CC[C@H](O[Si](C)(C)C(C)(C)C)C/C1=C\C=C1/CCC[C@@]2(C)[C@H]1CC[C@@H]2[C@H](C)CC[C@@H](O)C(C)(C)O[Si](C)(C)C(C)(C)C | 3927.1 | Semi standard non polar | 33892256 | | (24R)-24,25-Dihydroxycalciol,3TBDMS,isomer #1 | C=C1CC[C@H](O[Si](C)(C)C(C)(C)C)C/C1=C\C=C1/CCC[C@@]2(C)[C@H]1CC[C@@H]2[C@H](C)CC[C@@H](O[Si](C)(C)C(C)(C)C)C(C)(C)O[Si](C)(C)C(C)(C)C | 4180.7 | Semi standard non polar | 33892256 |
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| GC-MS Spectra| Spectrum Type | Description | Splash Key | Deposition Date | Source | View |
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| Predicted GC-MS | Predicted GC-MS Spectrum - (24R)-24,25-Dihydroxycalciol GC-MS (Non-derivatized) - 70eV, Positive | splash10-0a4i-7029200000-c84dd427774a8bd55bf4 | 2017-09-20 | Wishart Lab | View Spectrum | | Predicted GC-MS | Predicted GC-MS Spectrum - (24R)-24,25-Dihydroxycalciol GC-MS (3 TMS) - 70eV, Positive | splash10-014i-1312049000-f6115b14a152464f5e1b | 2017-10-06 | Wishart Lab | View Spectrum | | Predicted GC-MS | Predicted GC-MS Spectrum - (24R)-24,25-Dihydroxycalciol GC-MS (Non-derivatized) - 70eV, Positive | Not Available | 2021-10-12 | Wishart Lab | View Spectrum | | Predicted GC-MS | Predicted GC-MS Spectrum - (24R)-24,25-Dihydroxycalciol GC-MS (Non-derivatized) - 70eV, Positive | Not Available | 2021-10-12 | Wishart Lab | View Spectrum |
MS/MS Spectra| Spectrum Type | Description | Splash Key | Deposition Date | Source | View |
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| Predicted LC-MS/MS | Predicted LC-MS/MS Spectrum - (24R)-24,25-Dihydroxycalciol 10V, Positive-QTOF | splash10-00l2-0119200000-7bcd78fea8093a8230ae | 2017-10-06 | Wishart Lab | View Spectrum | | Predicted LC-MS/MS | Predicted LC-MS/MS Spectrum - (24R)-24,25-Dihydroxycalciol 20V, Positive-QTOF | splash10-0a5a-2369100000-04f3fb5d7d655a9ce470 | 2017-10-06 | Wishart Lab | View Spectrum | | Predicted LC-MS/MS | Predicted LC-MS/MS Spectrum - (24R)-24,25-Dihydroxycalciol 40V, Positive-QTOF | splash10-0zgi-4389100000-269c6b355710e7dcd9b8 | 2017-10-06 | Wishart Lab | View Spectrum | | Predicted LC-MS/MS | Predicted LC-MS/MS Spectrum - (24R)-24,25-Dihydroxycalciol 10V, Negative-QTOF | splash10-014i-0004900000-7bbe3ea5eae60b2a2059 | 2017-10-06 | Wishart Lab | View Spectrum | | Predicted LC-MS/MS | Predicted LC-MS/MS Spectrum - (24R)-24,25-Dihydroxycalciol 20V, Negative-QTOF | splash10-05mk-0009300000-4137913e2e1e7271894c | 2017-10-06 | Wishart Lab | View Spectrum | | Predicted LC-MS/MS | Predicted LC-MS/MS Spectrum - (24R)-24,25-Dihydroxycalciol 40V, Negative-QTOF | splash10-0079-9006000000-b2d6915fde38c349870a | 2017-10-06 | Wishart Lab | View Spectrum |
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| General References | - Thiele I, Swainston N, Fleming RM, Hoppe A, Sahoo S, Aurich MK, Haraldsdottir H, Mo ML, Rolfsson O, Stobbe MD, Thorleifsson SG, Agren R, Bolling C, Bordel S, Chavali AK, Dobson P, Dunn WB, Endler L, Hala D, Hucka M, Hull D, Jameson D, Jamshidi N, Jonsson JJ, Juty N, Keating S, Nookaew I, Le Novere N, Malys N, Mazein A, Papin JA, Price ND, Selkov E Sr, Sigurdsson MI, Simeonidis E, Sonnenschein N, Smallbone K, Sorokin A, van Beek JH, Weichart D, Goryanin I, Nielsen J, Westerhoff HV, Kell DB, Mendes P, Palsson BO: A community-driven global reconstruction of human metabolism. Nat Biotechnol. 2013 May;31(5):419-25. doi: 10.1038/nbt.2488. Epub 2013 Mar 3. [PubMed:23455439 ]
- Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
- Watson AD: Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Lipidomics: a global approach to lipid analysis in biological systems. J Lipid Res. 2006 Oct;47(10):2101-11. Epub 2006 Aug 10. [PubMed:16902246 ]
- Sethi JK, Vidal-Puig AJ: Thematic review series: adipocyte biology. Adipose tissue function and plasticity orchestrate nutritional adaptation. J Lipid Res. 2007 Jun;48(6):1253-62. Epub 2007 Mar 20. [PubMed:17374880 ]
- Lingwood D, Simons K: Lipid rafts as a membrane-organizing principle. Science. 2010 Jan 1;327(5961):46-50. doi: 10.1126/science.1174621. [PubMed:20044567 ]
- Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.
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