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SYBR Green I

Athanor · official

C32H37N4S+ · 509.7 g/mol

IUPAC name: N,N-dimethyl-N'-[4-[(Z)-(3-methyl-1,3-benzothiazol-2-ylidene)methyl]-1-phenylquinolin-1-ium-2-yl]-N'-propylpropane-1,3-diamine

Also called SYBR Green, asymmetric cyanine dye, dsDNA stain, qPCR dye

Reagents
Open in Athanor
The structure of SYBR Green I
Drawn from its SMILES with RDKit

Names and identifiers

IUPAC name
N,N-dimethyl-N'-[4-[(Z)-(3-methyl-1,3-benzothiazol-2-ylidene)methyl]-1-phenylquinolin-1-ium-2-yl]-N'-propylpropane-1,3-diamine
Synonyms
SYBR Green, asymmetric cyanine dye, dsDNA stain
+ 8 more

qPCR dye, SCHEMBL16758374, (E)-2-((2-((3-(dimethylamino)propyl)(propyl)amino)-1-phenylquinolin-4(1H)-ylidene)methyl)-3-methylbenzo[d]thiazol-3-ium, 2-[N-(3-dimethylaminopropyl)-N-propylamino]-4-[2,3-dihydro-3-methyl-(benzo-1,3-thiazol-2-yl)-methylidene]-1-phenyl-quinolinium, 2-{(E)-[2-{[3-(dimethylamino)propyl](propyl)amino}-1-phenylquinolin-4(1H)-ylidene]methyl}-3-methyl-1,3-benzothiazol-3-ium, 2-{[3-(dimethylamino)propyl](propyl)amino}-4-[(E)-(3-methyl-1,3-benzothiazol-2(3H)-ylidene)methyl]-1-phenylquinolinium, TD0001, 2-((3-(Dimethylamino)propyl)(propyl)amino)-4-((3-methylbenzo[d]thiazol-2(3H)-ylidene)methyl)-1-phenylquinolin-1-ium

Molecular formula
C32H37N4S+
Empirical formula
C32H37N4S
Molecular weight
509.7 g/mol
Exact mass
509.27389
CAS number
163795-75-3
PubChem CID
57448928
Canonical SMILES
CCCN(CCCN(C)C)C1=[N+](C2=CC=CC=C2C(=C1)C=C3N(C4=CC=CC=C4S3)C)C5=CC=CC=C5
Isomeric SMILES
CCCN(CCCN(C)C)C1=[N+](C2=CC=CC=C2C(=C1)/C=C\3/N(C4=CC=CC=C4S3)C)C5=CC=CC=C5
InChI
InChI=1S/C32H37N4S/c1-5-20-35(22-13-21-33(2)3)31-23-25(24-32-34(4)29-18-11-12-19-30(29)37-32)27-16-9-10-17-28(27)36(31)26-14-7-6-8-15-26/h6-12,14-19,23-24H,5,13,20-22H2,1-4H3/q+1
InChIKey
CGNLCCVKSWNSDG-UHFFFAOYSA-N
Molfile

Names, InChI and the identifiers from PubChem, retrieved 2026-10-14.

Calculated

Heavy atoms
37
Rings
5
Aromatic rings
4
Fraction sp³ carbons (Fsp3)
0.28
H-bond donors
0
H-bond acceptors
4
Rotatable bonds
9
TPSA (Ų)
13.6 computed here · PubChem 38.9
Formal charge
1
XLogP3
8.2 PubChem
Complexity
734 PubChem
Stereocenters
None
Double-bond geometry
C14=C15: Z
Point group
C1 of one 3D conformer with its hydrogens, by Athanor’s engine (as in the app)

Elemental analysis

  • C75.40%
  • H7.32%
  • N10.99%
  • S6.29%

Isotope pattern

100%509.27437%510.27711%511.2762.5%512.276513.277

Each peak is a nominal mass with its abundance-weighted exact mass, as a percentage of the tallest, from IUPAC natural isotope abundances.

Computed from the structure with RDKit 2026.09 when this page was built, beside PubChem's own computed values from its record; where the two differ, both are shown.

Predicted

log P
6.83 Crippen (Wildman and Crippen 1999)
log S (water solubility)
-7.15 ESOL (Delaney 2004), log mol/L
Synthetic accessibility
3.07 SA score, 1 easy to 10 hard (Ertl and Schuffenhauer 2009)

Drug-likeness: Lipinski’s rule of five

  • Molecular weight ≤ 500: 509.74
  • log P ≤ 5 (Crippen): 6.83
  • H-bond donors ≤ 5: 0
  • H-bond acceptors ≤ 10: 4

Breaks 2 of the four rules.

¹³C NMR shifts, predicted

Predictions, not measurements; each names its method. A measured log P, where a source reports one, is under Physical properties.

Safety

No GHS hazard classification was found in the sources.

Safety data sheets on the supplier’s page: Molport, BLD Pharm, TargetMol.

Always read the supplier’s safety data sheet before working with it.

Literature

Reading PubChem, OpenAlex and GSRS…

Bioactivity

Reading ChEMBL…

References

  1. ·Calculated values: computed by Athanor with RDKit 2026.09 from the structure.
  2. ·Literature on PubChem

Data last updated 2026-10-14.