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Structure of 2450-71-7
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The BI-3802 was designed by Boehringer Ingelheim and could be obtained free of charge through the Boehringer Ingelheim open innovation portal opnMe.com, associated with its negative control.
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Enrichable Protein Footprinting for Structural Proteomics
Wolfer, Jamison D ; Minkoff, Benjamin B ; Burch, Heather L ; Sussman, Michael R ;
Abstract: Protein footprinting is a useful method for studying protein higher order structure and conformational changes induced by interactions with various ligands via addition of covalent modifications onto the protein. Compared to other methods that provide single amino acid-level structural resolution, such as cryo-EM, X-ray diffraction, and NMR, mass spectrometry (MS)-based methods can be advantageous as they require lower protein amounts and purity. As with other MS-based proteomic methods, such as post-translational modification analysis, enrichment techniques have proven necessary for both optimal sensitivity and sequence coverage when analyzing highly complex proteomes. Currently used reagents for footprinting via covalent labeling, such as hydroxyl radicals and carbodiimide-based methods, do not yet have a suitable enrichment method, limiting their applicability to whole proteome analysis. Here, we report a method for enrichable covalent labeling built upon the GEE/EDC system commonly used to covalently label aspartic acid and glutamic acid residues. Novel labeling reagents containing alkynyl functionality can be "clicked" to any azido-containing molecule with copper-catalyzed azide−alkyne cycloaddition (CuAAC), allowing for enrichment or further labeling. Multiple azide- and alkyne-containing GEE-like molecules were tested, and the most efficient method was determined to be the EDC-facilitated coupling of glycine propargyl amide (GPA) to proteins. The pipeline we report includes clicking via CuAAC to a commercially available biotin-azide containing a photocleavable linker, followed by enrichment using a streptavidin resin and subsequent cleavage under ultraviolet light. The enrichment process was optimized through the screening of clickable amines, coupling reagents, and enrichment scaffolds and methods with pure model proteins and has also been applied to complex mixtures of proteins isolated from the model plant, Arabidopsis thaliana, suggesting that our method may ultimately be used to measure protein conformation on a proteomic scale.
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Purchased from AmBeed: 1221722-25-3 ; 1895922-69-6 ; 2450-71-7 ; 3945-69-5 ; 26557-78-8 ; 944561-44-8 ; 54060-30-9 ; 15252-44-5 ; 14044-63-4 ; 122116-12-5
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CAS No. : | 2450-71-7 |
Formula : | C3H5N |
M.W : | 55.08 |
SMILES Code : | C#CCN |
MDL No. : | MFCD00008198 |
InChI Key : | JKANAVGODYYCQF-UHFFFAOYSA-N |
Pubchem ID : | 239041 |
GHS Pictogram: |
![]() ![]() ![]() |
Signal Word: | Danger |
Hazard Statements: | H225-H302-H310-H314 |
Precautionary Statements: | P210-P280-P302+P350-P305+P351+P338-P310 |
Class: | 3(6.1,8) |
UN#: | 3286 |
Packing Group: | Ⅱ |
Num. heavy atoms | 4 |
Num. arom. heavy atoms | 0 |
Fraction Csp3 | 0.33 |
Num. rotatable bonds | 0 |
Num. H-bond acceptors | 1.0 |
Num. H-bond donors | 1.0 |
Molar Refractivity | 17.4 |
TPSA ? Topological Polar Surface Area: Calculated from |
26.02 Ų |
Log Po/w (iLOGP)? iLOGP: in-house physics-based method implemented from |
1.38 |
Log Po/w (XLOGP3)? XLOGP3: Atomistic and knowledge-based method calculated by |
-0.43 |
Log Po/w (WLOGP)? WLOGP: Atomistic method implemented from |
-0.34 |
Log Po/w (MLOGP)? MLOGP: Topological method implemented from |
0.15 |
Log Po/w (SILICOS-IT)? SILICOS-IT: Hybrid fragmental/topological method calculated by |
-0.37 |
Consensus Log Po/w? Consensus Log Po/w: Average of all five predictions |
0.08 |
Log S (ESOL):? ESOL: Topological method implemented from |
0.09 |
Solubility | 67.7 mg/ml ; 1.23 mol/l |
Class? Solubility class: Log S scale |
Highly soluble |
Log S (Ali)? Ali: Topological method implemented from |
0.35 |
Solubility | 123.0 mg/ml ; 2.23 mol/l |
Class? Solubility class: Log S scale |
Highly soluble |
Log S (SILICOS-IT)? SILICOS-IT: Fragmental method calculated by |
0.18 |
Solubility | 83.9 mg/ml ; 1.52 mol/l |
Class? Solubility class: Log S scale |
Soluble |
GI absorption? Gatrointestinal absorption: according to the white of the BOILED-Egg |
Low |
BBB permeant? BBB permeation: according to the yolk of the BOILED-Egg |
No |
P-gp substrate? P-glycoprotein substrate: SVM model built on 1033 molecules (training set) |
No |
CYP1A2 inhibitor? Cytochrome P450 1A2 inhibitor: SVM model built on 9145 molecules (training set) |
No |
CYP2C19 inhibitor? Cytochrome P450 2C19 inhibitor: SVM model built on 9272 molecules (training set) |
No |
CYP2C9 inhibitor? Cytochrome P450 2C9 inhibitor: SVM model built on 5940 molecules (training set) |
No |
CYP2D6 inhibitor? Cytochrome P450 2D6 inhibitor: SVM model built on 3664 molecules (training set) |
No |
CYP3A4 inhibitor? Cytochrome P450 3A4 inhibitor: SVM model built on 7518 molecules (training set) |
No |
Log Kp (skin permeation)? Skin permeation: QSPR model implemented from |
-6.94 cm/s |
Lipinski? Lipinski (Pfizer) filter: implemented from |
0.0 |
Ghose? Ghose filter: implemented from |
None |
Veber? Veber (GSK) filter: implemented from |
0.0 |
Egan? Egan (Pharmacia) filter: implemented from |
0.0 |
Muegge? Muegge (Bayer) filter: implemented from |
3.0 |
Bioavailability Score? Abbott Bioavailability Score: Probability of F > 10% in rat |
0.55 |
PAINS? Pan Assay Interference Structures: implemented from |
0.0 alert |
Brenk? Structural Alert: implemented from |
1.0 alert: heavy_metal |
Leadlikeness? Leadlikeness: implemented from |
No; 1 violation:MW<1.0 |
Synthetic accessibility? Synthetic accessibility score: from 1 (very easy) to 10 (very difficult) |
2.14 |
* All experimental methods are cited from the reference, please refer to the original source for details. We do not guarantee the accuracy of the content in the reference.
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
With sodium acetate; In water; acetic anhydride; acetic acid; | Example 14 N-propargylmaleimide (22): A solution of maleic anhydride (19, 2.5 g, 25.5 mmol) and propargylamine (20, 1.75 mL, 25.5 mmol) in glacial acetic acid (50 mL) was stirred in the dark overnight. The reaction mixture was concentrated to dryness and the residue was recrystallized from a mixture of isopropyl alcohol and water. This gave 21 (3.079 g, 20.1 mmol, 79%) as white crystals. Compound 21 (1.49 g, 9.70 mmol) was suspended in acetic anhydride (7 mL) and sodium acetate (437 mg, 5.33 mmol) was added. The resulting suspension was stirred at 65 C. for 2 h, cooled down to room temperature, and then poured into ice-cold water (75 mL). The aqueous solution was extracted three times with diethyl ether. The combined organic layers were dried over Na2SO4, filtered, and concentrated. Column chromatography (CH2Cl2/EtOAc=1/1) provided 22 (755 mg, 5.59 mmol, 58%) as an off-white solid. 1H NMR (400 MHz, CDCl3) delta: 2.21 (t, 1H, J=2.6 Hz, ?C-H), 4.30 (d, 2H, J=2.6 Hz, CH2), 6.76 (s, 2H, =C-H). |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
468 mg | In methanol; for 5h;Reflux; | 6.01.35.02 3-methyl-5,6,8,9-tetrahydro-imidazo[1,2-a][1,4]diazepine-7-carboxylic acid tert-butyl ester 0.6 mL propargylamin was added to 429 mg <strong>[190900-21-1]5-oxo-[1,4]diazepane-1-carboxylic acid tert-butyl ester</strong> in 20 mL methanol. The reaction was refluxed 5 h and evaporated to give 468 mg of the desired product. (M+H)+: 252, Rt: 0.88 min (method J) |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
88% | With triethylamine; N-[(dimethylamino)-3-oxo-1H-1,2,3-triazolo[4,5-b]pyridin-1-yl-methylene]-N-methylmethanaminium hexafluorophosphate; In N,N-dimethyl-formamide; at 20℃; for 22h;Inert atmosphere; Cooling with ice; | General procedure: Alkynylamine (1.5equiv) was added to N-Boc-l-leucine or N-Boc-l-beta-homoleucine (1equiv) and HATU (1.1equiv) in DMF at room temperature under nitrogen. The solutions were cooled on ice and Et3N (3equiv) was added, thereaction mixture was then allowed to reach room temperature and stirred for 22h. The reaction mixture was diluted with EtOAc(30ml), washed with 0.1M HCl (2×10ml), saturated NaHCO3 (10ml), brine (20ml), dried over Na2SO4 and the solvents wereremoved. The crude product was purified by automated flashchromatography (gradient, 0-100% EtOAc in heptane). |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
91% | With triethylamine; dicyclohexyl-carbodiimide; In dichloromethane; at 20℃; for 1h;Inert atmosphere; | Boc-L-Asp(OMe)-OH 15 (2 g,8.1 mmol) and 40 mL DCM were taken in a 100 mL round bottom flask and cooled at0C. To this solution DCC (1.67 g, 8.1 mmol) and propargylamine (450 mg, 8.1mmole) was added. The reaction mixture was stirred for 1 hour at rt. Thereaction was monitored by TLC and showed the complete disappearance of startingmaterial. The resultant white mixture was filtered to remove 1, 3dicyclohexyleurea. Filtrate was concentrated and purified by columnchromatography using DCM/MeOH (98.5:1.5) as eluent to obtain compound 16 as a white solid. (2.1 g, 91%). [alpha]21D = 26 (c 0.1, CHCl3). 1HNMR: (CDCl3, 400 MHz) 1.38 (s, 9H), 2.20 (t, 1H, J = 2.44 Hz), 2.69 (dd, 1H, J = 4.36 Hz, J = 15.8 Hz), 2.86 (dd, 1H, J= 4.72 Hz, J = 15.84 Hz), 3.69 (s,3H), 3.95-3.97 (m, 2H), 4.47-4.49 (m, 1H), 5.76-5.78 (d, 1H, J = 8.4 Hz), 6.76 (t, 1H, J = 4.68 Hz). 13C NMR: (CDCl3,100 MHz) 28.3, 29.1, 37.6, 50.3, 52.7,71.6, 79.4, 80.0, 155.7, 169.8, 172.01. IR (KBr) 3301, 2979, 1709, 1660, 1528, 1438, 1393, 1368, 1347, 1251, 1166,1056, 1029, 861, 762, 661 cm-1. HRMS (ESI): m/z calcd. for C13H21N2O5[M+H]+ 285.1445; found 285.1450. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
86% | In a 50 mL round-bottom flask freshly prepared TMP-CHO (150 mg 1 mmol) was added and dissolved in 20 mL of 1 2-dichloroethane propargylamine (66 mg 1.2 mmol) was added slowly at room temperature the reaction was run at at room temperature for 2 hours triacetoxy sodium borohydride (424 mg 2 mmol) was added and monitored by TLC about 2 hours later the reaction was complete 10 mL of 10 K2CO3was added for quenching. The resulting material was extracted with dichloromethane dried over anhydrous sodium sulfate filtered and concentrated and purified with silica gel column chromatography (ethyl acetatepetroleum ether 32) to give the compound MT-012 as a yellow solid (163mg 86) . ESI-MS [M+H]+m/z 190.3.1H-NMR (CDCl3) 3.96 (s 2H) 3.56 (d J2.4 Hz 2H) 2.51 (s 3H) 2.49 (s 6H) 2.26 (t J2.4 Hz 1H) . | |
86% | In 1,2-dichloro-ethane; at 20℃; for 2h; | 10110] In a 50 mE round-bottom flask, freshly prepared TMP-CHO(lSOmg, 1 mmol)was addedanddissolvedin20 mE of 1 ,2-dichloroethane, propargylamine (66 mg, 1.2 mmol) was added slowly at room temperature, the reaction was run at room temperature for 2 hours, triacetoxy sodium borohydride (424 mg, 2 mmol) was added and monitored by TEC, about 2 hours later the reaction was complete, 10 mE of 10% K2C03 was added for quenching. The resulting material was extracted with dichloromethane, dried over anhydrous sodium sulfate, filtered and concentrated, and purified with silica gel colunm chromatography (ethyl acetate:petroleum ether 3:2) to give the compound MT-012 as a yellow solid (163 mg, 86%). ESI-MS: [M+H] mlz 190.3. ?H-NMR (CDC13): 3.96 (s, 2H); 3.56 (d, J=2.4 Hz, 2H); 2.51 (s, 3H); 2.49 (s, 6H); 2.26 (t, J=2.4 Hz, 1H). |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
68% | With montmorillonite K-10; In ethanol; at 80℃; for 0.5h;Sealed tube; Microwave irradiation; | General procedure: To a solution of 1 (2.0 mmol) in absolute EtOH (8.0 mL)in a glass tube was added dropwise the appropriate amine(3.6 mmol) and K-10 (0.3 g mmol-1); the quartz tubewas sealed with reaction mixture and introduced intoa microwave oven. The flask was irradiated for 30 min(150 W) the temperature of 80 C. After completion of thereaction the mixture was filtered, the organic phase wasdried with Na2SO4, filtered and the solvent was evaporatedunder reduced pressure to give the crude products. All thecompounds were purified by column chromatographyon silica gel using 2-5% EtOH-CH2Cl2 as eluent to giveanalytically pure products 3a-m. The products werecharacterized by corresponding spectroscopic data (1H and13C NMR, and HRMS). |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
30% | To a stirred solution of <strong>[1189513-51-6]5-bromo-3-chloropicolinic acid</strong> (10 g, 42.3 mmol) in DMF (100 mL) was added HOBT (3.24 g, 21.15 mmol), EDCI (6.57 g, 42.3 mmol) and Et3N (11.79 mL, 85 mmol) and the reaction mixture was allowed to stir for 30 min. Thereafter prop-2-yn-1-amine (3.30 mL, 51.6 mmol) was added and reaction mixture was allowed to stir for 14 h at 25eC. Upon completion, reaction mixture was quenched with water (500 mL) and aqueous phase was extracted with ethyl acetate (200 mL x 3), combined organic layer was dried over anhydrous sodium sulphate and filtered. The filtrate was rotary evaporated and residue was purified by flash column chromatography (silica gel) to afford 3.50 g (30percent) of the titled product as a white solid. 1HNMR (400 MHz, DMSO-d6) U9.12 (t, J = 6.0 Hz, 1H), 8.73 (s, 1H), 8.48 (s, 1H), 4.12 ' 3.98 (m, 2H), 3.17 (s, 1H). ESI-MS (m/z) 274.9 (MH)\ |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
To a solution of propargylamine (3.2 mL, 50 mmol) in aqueous HC1 soulution (1.0 N, 50 mL) was added KOCN (16 g, 200 mmol) at r.t. After stirring overnight at 60 C, the mixture was cooled to 0 C to give a white precipitate. After filtration, the solid was dissolved in MeOH (150 ml) and stirred with silica gel (25 g) for 6 h. The mixture was then filtered and concentrated under vacuum to give the desired urea 4a as a white solid (3.5 g, 71%) without further purification. NMR (400 MHz, MeOD) delta 3.88 (d, J = 2.5 Hz, 2H), 2.54 (t, J = 2.5 Hz, 1H). 13C NMR (126 MHz, MeOD) delta 161.55, 81.63, 71.80, 30.18. m/z HRMS (ESI) found [M+H]+ 99.0552, C4HvN20+ requires 99.0553. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
95% | With N-ethyl-N,N-diisopropylamine; N-[(dimethylamino)-3-oxo-1H-1,2,3-triazolo[4,5-b]pyridin-1-yl-methylene]-N-methylmethanaminium hexafluorophosphate; In N,N-dimethyl-formamide; at 25℃; for 6h;Inert atmosphere; | To a solution of <strong>[80286-58-4]artemisinic acid</strong> (1), (100 mg, 1 equiv), HATH (191 mg, 1.2 equiv) and DIPEA (87 pL, 1.2 equiv) in DMF (10 mL) was added propargyl amine (32 pL, 1.2 equiv) at 25 C under a argon atmosphere. The mixture was stirred for 6 h. After completion of reaction (TLC), the solvent was removed in vacuo and the resulting oil residue was diluted with DCM (15 mL) and extracted with water. The combined DCM layers were dried over Na2S04 filtered and concentrated. The crude product was purified by flash chromatography to give compound 3 (109 mg) in 95% yield. 1H NMR (500 MHz, CDCl3) d = 6.29 (brs, 1H), 5.63 (s, 1H), 5.15 (s, 1H), 4.96 (s, 1H), 4.16 - 4.11 (m, 1H), 4.03 - 3.98 (m, 1H), 2.74 (d, J= 12.6 Hz, 1H), 2.42 (s, 1H), 2.23 (t, 7= 2.7 Hz, 1H), 2.15 (s, 1H), 1.90 - 1.85 (m, 2H), 1.75 - 1.66 (m, 2H), 1.57 (s, 3H), 1.56 -1.49 (m, 1H), 1.44 - 1.37 (m, 3 H), 1.29 - 1.23 (m, 1H), 0.86 (d, J = 5.3 Hz, 3H). 13C NMR (125 MHz, CDCl3) d = 169.5, 148.7, 135.1, 120.2, 116.6, 79.6, 71.6, 42.6, 41.2, 37.7, 35.0, 29.4, 27.5, 26.4, 25.4, 25.3, 23.7, 19.7. HRMS (ESI): m/z calcd for [M+H]+, CI8H26ON 272.2009 found 272.2004 |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
In methanol; at 100℃; for 4h;Microwave irradiation; | To a solution of <strong>[34231-77-1]methyl pyridazine-4-carboxylate</strong> (1 g) in methanol (2.5 ml_) was added prop-2-yn-1- amine (4 g) and the mixture was heated at 100C under microwave irradiation for 4 hours. After cooling to room temperature, the reaction mixture was concentrated and purified by silica gel chromatography eluting with 90-100% ethyl acetate in cyclohexane to afford A/-prop-2-ynylpyridazine- 4-carboxamide as white solid. (0804) NMR (400MHz, DMSO-de) 9.53-9.56 (m, 1 H) 9.47-9.52 (m, 1 H) 9.42-9.46 (m, 1 H) 7.96-8.03 (m, 1 H) 4.06-4.16 (m, 2H) 3.19-3.26 (m, 1 H) |