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Fluorescent dyes and stains

CypHer5

Also known as 6-{2-[5-(3,3-dimethyl-5-sulfo-3H-indol-2-yl)penta-2,4-dien-1-ylidene]-3,3-dimethyl-5-sulfo-2,3-dihydro-1H-indol-1-yl}hexanoic acid, 2-[5-(3,3-Dimethyl-5-sulfo-3H-indol-2-yl)-2,4-pentadien-1-ylidene]-2,3-dihydro-3,3-dimethyl-5-sulfo-1H-indole-1-hexanoic acid

Formula C31H36N2O8S2Molar mass 628.77 g/mol
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CypHer5 chemical structure, C31H36N2O8S2
2D chemical structure

Key facts

What buyers check first

All properties
Formula
C31H36N2O8S2
Molar mass
628.77 g/mol
HS code
293399
Category
Fluorescent dyes and stains

What is CypHer5?

Plain description, key identifiers and synonyms

CypHer5 is a C5-cyanine dye having differentially-substituted 2-indolyl units at each end. It has a role as a fluorochrome.

Identifiers

Registry numbers, names and line notations, tap to copy

IUPAC name
6-[(2Z)-2-[(2E,4E)-5-(3,3-dimethyl-5-sulfoindol-2-yl)penta-2,4-dienylidene]-3,3-dimethyl-5-sulfoindol-1-yl]hexanoic acid
Molecular formula
C31H36N2O8S2
InChIKey
VRQVBVFJEIJSIE-BXPMDSANSA-N
InChI
InChI=1S/C31H36N2O8S2/c1-30(2)23-19-21(42(36,37)38)14-16-25(23)32-27(30)11-7-5-8-12-28-31(3,4)24-20-22(43(39,40)41)15-17-26(24)33(28)18-10-6-9-13-29(34)35/h5,7-8,11-12,14-17,19-20H,6,9-10,13,18H2,1-4H3,(H,34,35)(H,36,37,38)(H,39,40,41)/b8-5+,11-7+,28-12-
Canonical SMILES
CC1(C)C(C=CC=CC=C2N(CCCCCC(=O)O)c3ccc(S(=O)(=O)O)cc3C2(C)C)=Nc2ccc(S(=O)(=O)O)cc21
Isomeric SMILES
CC1(C2=C(C=CC(=C2)S(=O)(=O)O)N=C1/C=C/C=C/C=C\3/C(C4=C(N3CCCCCC(=O)O)C=CC(=C4)S(=O)(=O)O)(C)C)C

Synonyms

  • 6-{2-[5-(3,3-dimethyl-5-sulfo-3H-indol-2-yl)penta-2,4-dien-1-ylidene]-3,3-dimethyl-5-sulfo-2,3-dihydro-1H-indol-1-yl}hexanoic acid
  • 2-[5-(3,3-Dimethyl-5-sulfo-3H-indol-2-yl)-2,4-pentadien-1-ylidene]-2,3-dihydro-3,3-dimethyl-5-sulfo-1H-indole-1-hexanoic acid

Physical and chemical properties

Measured values and descriptors computed from the structure

Physical and chemical properties

Measured values, check the supplier specification for your grade

No measured properties are recorded for this substance yet. Ask suppliers for a technical data sheet.

Values vary by grade. Ask suppliers for the COA or TDS of the batch you buy.

Computed descriptors

Calculated from the structure, useful for screening and formulation

Molecular weight
628.77 g/molcalc.
Exact mass
628.1913 Dacalc.
LogP (octanol/water)
5.98calc.
Topological polar surface area
161.6 Ųcalc.
Hydrogen bond donors
3calc.
Hydrogen bond acceptors
7calc.
Rotatable bonds
11calc.
Heavy atoms
43calc.
Rings
4calc.
Aromatic rings
2calc.
Fraction sp3 carbons
0.36calc.
Formal charge
0calc.
Stereocentres
0calc.
Lipinski rule of five
Fails (2 violations)calc.

Calculated for screening. Confirm critical figures with the supplier.

Murcko scaffold

The ring system that remains when every side chain is removed

Murcko scaffold of this chemical, C(=CC=C1Cc2ccccc2N1)C=CC1=Nc2ccccc2C1

C(=CC=C1Cc2ccccc2N1)C=CC1=Nc2ccccc2C1

4 rings, 23 atoms.

249 other chemicals share this scaffold

Safety and hazards

GHS classification summary, not a safety data sheet

No GHS hazard classification is recorded for this substance yet. That does not mean it is harmless.

GHS classification summary, not a safety data sheet (SDS). Classifications can differ by supplier, grade and concentration. Always check the supplier's SDS.

CypHer5 suppliers

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CypHer5 price

Indicative price range per kg from live supplier offers

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Suppliers quote this chemical on request. Send one free request and compare quotes side by side.

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Uses and applications

What the substance is used for, by industry and function

Roles

  • dye
  • fluorescent dye
  • fluorochrome

Regulatory status

Inventories, regulations and trade controls that list this substance

No regulatory list memberships are recorded for this substance yet. Always check the rules of the importing and exporting country before trade.

HS code and trade data

Customs classification and reported world trade statistics

Global trade

World import and export statistics for the HS code CypHer5 is traded under.

HS 2933.99Indicative HS code

Heterocyclic compounds with nitrogen hetero-atom(s) only, other

World exports in 2024
$12.1B
−31.0% vs 2023, imports $28.8B
2019 to 2024
Top exporters
  1. China30.5%
  2. India * partner reported16.3%
  3. Ireland9.0%
Top importers
  1. Slovenia31.7%
  2. Italy24.2%
  3. United States5.0%

* Partner reported figures, a lower bound.

Reported customs values in USD, not prices.Full trade data

The HS code shown for CypHer5 is indicative (it was assigned by structure rules). Confirm the classification with your customs broker before shipping.

Frequently asked questions

Quick answers about CypHer5, based on the data on this page

What is CypHer5?

CypHer5 is a C5-cyanine dye having differentially-substituted 2-indolyl units at each end. It has a role as a fluorochrome.

What is the molecular formula and weight of CypHer5?

The molecular formula of CypHer5 is C31H36N2O8S2 and its molar mass is 628.77 g/mol.

What is CypHer5 used for?

Known uses and roles of CypHer5 include dye, fluorescent dye and fluorochrome.

Is CypHer5 hazardous?

No GHS hazard classification for CypHer5 is recorded on CompoundList yet. That does not prove it is safe. Always read the supplier safety data sheet.

What is the HS code of CypHer5?

CypHer5 is usually classified under HS code 293399 (Heterocyclic compounds with nitrogen hetero-atom(s) only, other). This is indicative, confirm it with your customs broker before shipping.

Where can I buy CypHer5?

Post a free request on CompoundList and suppliers of CypHer5 will send you quotes. Your contact details stay private until you accept a quote.

What is the price of CypHer5?

Suppliers quote CypHer5 on request because prices depend on grade, purity, quantity and destination. A free request on CompoundList gets you several quotes to compare.

Guides for buyers

Practical guides that help when you source, ship or handle CypHer5

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Data last updated 7 Oct 2026. Details may have changed, please confirm them with the supplier. Report an error on this page
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