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Structure of Cy3 (C31H38N2O8S2)

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2D chemical structure image of Cy3
Chemical Formula C31H38N2O8S2
Molecular Weight 630.77202 g/mol
IUPAC Name 1-(5-carboxypentyl)-2-[(1E)-3-[(2Z)-1-ethyl-3,3-dimethyl-5-sulfonato-2,3-dihydro-1H-indol-2-ylidene]prop-1-en-1-yl]-3,3-dimethyl-5-sulfo-3H-indol-1-ium
SMILES String CCN3C(=CC=CC2=[N+](CCCCCC(O)=O)c1ccc(cc1C2(C)C)S(O)(=O)=O)C(C)(C)c4cc(ccc34)S([O-])(=O)=O
InChI InChI=1S/C31H38N2O8S2/c1-6-32-25-16-14-21(42(36,37)38)19-23(25)30(2,3)27(32)11-10-12-28-31(4,5)24-20-22(43(39,40)41)15-17-26(24)33(28)18-9-7-8-13-29(34)35/h10-12,14-17,19-20H,6-9,13,18H2,1-5H3,(H2-,34,35,36,37,38,39,40,41)
InChIKey YDNYBBRGPORVRT-UHFFFAOYSA-N
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Chemical Structure Description

A chemical structure of a molecule includes the arrangement of atoms and the chemical bonds that hold the atoms together. The Cy3 molecule contains a total of 84 bond(s). There are 46 non-H bond(s), 20 multiple bond(s), 11 rotatable bond(s), 8 double bond(s), 12 aromatic bond(s), 2 five-membered ring(s), 2 six-membered ring(s), 2 nine-membered ring(s), 1 carboxylic acid(s) (aliphatic), 1 tertiary amine(s) (aromatic), 1 positively charged N, 2 hydroxyl group(s), 1 sulfonic (thio-/dithio-) acid(s), and 1 sulfonate(s) (thio-/dithio-). Images of the chemical structure of Cy3 are given below:

2D chemical structure image of Cy3
2-dimensional (2D) chemical structure image of Cy3
3D chemical structure image of Cy3
3-dimensional (3D) chemical structure image of Cy3

The 2D chemical structure image of Cy3 is also called skeletal formula, which is the standard notation for organic molecules. The carbon atoms in the chemical structure of Cy3 are implied to be located at the corner(s) and hydrogen atoms attached to carbon atoms are not indicated – each carbon atom is considered to be associated with enough hydrogen atoms to provide the carbon atom with four bonds.

The 3D chemical structure image of Cy3 is based on the ball-and-stick model which displays both the three-dimensional position of the atoms and the bonds between them. The radius of the spheres is therefore smaller than the rod lengths in order to provide a clearer view of the atoms and bonds throughout the chemical structure model of Cy3. Download structure data file (SDF/MOL) file of this compound.

Interactive 3D Visualization

For a better understanding of the chemical structure, an interactive 3D visualization of Cy3 is provided here.

The Cy3 molecule shown in the visualization screen can be rotated interactively by keep clicking and moving the mouse button. Mouse wheel zoom is available as well – the size of the Cy3 molecule can be increased or decreased by scrolling the mouse wheel.

The information of the atoms, bonds, connectivity and coordinates included in the chemical structure of Cy3 can easily be identified by this visualization. By right-clicking the visualization screen, various other options are available including the visualization of van der Waals surface and exporting to an image file.

Search Another Chemical Structure

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Input a chemical compound consisting of C, H, N, O, S, F, Cl, Br, I, Si, P, and/or As atom(s)

Input example for Ethanol:

  • Name: ethanol
  • CAS #: 64-17-5
  • Formula: C2H5OH
  • Smiles: CCO
  • InChI: InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3
  • InChIKey: LFQSCWFLJHTTHZ-UHFFFAOYSA-N

Additional Information for Identifying Cy3 Molecule

  • SMILES (Simplified Molecular-Input Line-Entry System) string of Cy3

    The SMILES string of Cy3 is CCN3C(=CC=CC2=[N+](CCCCCC(O)=O)c1ccc(cc1C2(C)C)S(O)(=O)=O)C(C)(C)c4cc(ccc34)S([O-])(=O)=O, which can be can be imported by most molecule editors for conversion back into two-dimensional drawings or three-dimensional models of the Cy3.

  • Structure Data File (SDF/MOL File) of Cy3

    The structure data file (SDF/MOL File) of Cy3 is available for download in the SDF page of Cy3, which provides the information about the atoms, bonds, connectivity and coordinates of Cy3. The Cy3 structure data file can be imported to most of the cheminformatics software systems and applications.

  • Chemical formula of Cy3

    The molecular formula of Cy3 is available in chemical formula page of Cy3, which identifies each constituent element by its chemical symbol and indicates the proportionate number of atoms of each element.

  • Molecular weight of Cy3

    The molecular weight of Cy3 is available in molecular weight page of Cy3, which is calculated as the sum of the atomic weights of each constituent element multiplied by the number of atoms of that element in the molecular formula.

  • Other names (synonyms) or registry numbers of Cy3

    The Cy3 compound may be called differently depending on the various different situations of industrial applications. Below are the list of the other names (synonyms) of Cy3 including the various registry numbers, if available:

    • 2-((E)-3-((E)-1-(5-carboxypentyl)-3,3-dimethyl-5-sulfoindolin-2-ylidene)prop-1-en-1-yl)-1-ethyl-3,3-dimethyl-3H-indol-1-ium-5-sulfonate
    • ylidene)prop-1-en-1-yl)-1-ethyl-3,3-dimethyl-3H-indol-1-ium-5-sulfonate
    • 2-((E)-3-((E)-1-(5-carboxypentyl)-3,3-dimethyl-5-sulfoindolin-2-
    • MFCD28968789
    • Sulfo Cy3 Carboxylic acids
    • 2-(3-(1-(5-Carboxypentyl)-3,3-dimethyl-5-sulfoindolin-2-ylidene)prop-1-en-1-yl)-1-ethyl-3,3-dimethyl-3H-indol-1-ium-5-sulfonate
    • 146368-13-0
    • 2-((1E,3E)-3-(1-(5-carboxypentyl)-3,3-dimethyl-5-sulfoindolin-2-ylidene)prop-1-en-1-yl)-1-ethyl-3,3-dimethyl-3H-indol-1-ium-5-sulfonate
    • HY-D0822
    • Cy3

Cy3 Identification Summary Frequently Asked Questions (FAQs)

What’s the chemical formula of Cy3?
C31H38N2O8S2
How many atoms and what are the elements included the Cy3 molecule?
81 atom(s) - 38 Hydrogen atom(s), 31 Carbon atom(s), 2 Nitrogen atom(s), 8 Oxygen atom(s), and 2 Sulfur atom(s)
How many chemical bonds and what kind of bonds are included the Cy3 structure?
84 bond(s) - 46 non-H bond(s), 20 multiple bond(s), 11 rotatable bond(s), 8 double bond(s), 12 aromatic bond(s), 2 five-membered ring(s), 2 six-membered ring(s), 2 nine-membered ring(s), 1 carboxylic acid(s) (aliphatic), 1 tertiary amine(s) (aromatic), 1 positively charged N, 2 hydroxyl group(s), 1 sulfonic (thio-/dithio-) acid(s), and 1 sulfonate(s) (thio-/dithio-)
What’s the Cy3’s molecular weight?
630.77202 g/mol
What’s the SMILES code of Cy3?
CCN3C(=CC=CC2=[N+](CCCCCC(O)=O)c1ccc(cc1C2(C)C)S(O)(=O)=O)C(C)(C)c4cc(ccc34)S([O-])(=O)=O
What’s the InChI string of Cy3?
InChI=1S/C31H38N2O8S2/c1-6-32-25-16-14-21(42(36,37)38)19-23(25)30(2,3)27(32)11-10-12-28-31(4,5)24-20-22(43(39,40)41)15-17-26(24)33(28)18-9-7-8-13-29(34)35/h10-12,14-17,19-20H,6-9,13,18H2,1-5H3,(H2-,34,35,36,37,38,39,40,41)
What’s the InChIKey code of Cy3?
YDNYBBRGPORVRT-UHFFFAOYSA-N