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Dyes & imaging agents: 111 3D models

Water, gases, sugars, nucleotides, amino acids, ions (real sizes 0.1–1 nm). Each one is a ready-made 3D model you can turn, recolour and place in a figure — open BioDioRama and type its name in the Library search.

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Fluorescein — Bright green fluorophore (ex 494 / em 521 nm). C20H12O5, 332.3 g/mol. Real 3D structure from PubChem.
FITC — Amine-reactive FITC for labelling proteins and nanoparticles. Real 3D structure from PubChem.
Rhodamine B — Orange-red fluorescent dye. C28H31ClN2O3, 479 g/mol. Real 3D structure from PubChem.
Rhodamine 6G — C28H31ClN2O3, 479 g/mol. Real 3D structure from PubChem.
TRITC — C25H21N3O3S, 443.5 g/mol. Real 3D structure from PubChem.
DAPI — Blue nuclear stain that binds the DNA minor groove. C16H15N5, 277.32 g/mol. Real 3D structure from PubChem.
Hoechst 33342 — Cell-permeant blue DNA stain for live cells. C27H28N6O, 452.6 g/mol. Real 3D structure from PubChem.
Propidium iodide — Red DNA dye that only enters dead cells. C27H34I2N4, 668.4 g/mol. Real 3D structure from PubChem.
Ethidium bromide — C21H20BrN3, 394.3 g/mol. Real 3D structure from PubChem.
Indocyanine green — Near-infrared dye approved for imaging; also a photothermal agent. C43H47N2NaO6S2, 775 g/mol. Real 3D structure from PubChem.
Methylene blue — C16H18ClN3S, 319.9 g/mol. Real 3D structure from PubChem.
Nile red — Lipid-sensing dye; fluoresces in fat droplets and nanoparticle cores. C20H18N2O2, 318.4 g/mol. Real 3D structure from PubChem.
Coumarin — C9H6O2, 146.14 g/mol. Real 3D structure from PubChem.
7-hydroxycoumarin — C9H6O3, 162.14 g/mol. Real 3D structure from PubChem.
Calcein — C30H26N2O13, 622.5 g/mol. Real 3D structure from PubChem.
Calcein AM — Non-fluorescent ester turned green by esterases in live cells. C46H46N2O23, 994.9 g/mol. Real 3D structure from PubChem.
BODIPY FL — Real 3D structure from PubChem.
Cy5 — C33H40N2O8S2, 656.8 g/mol. Real 3D structure from PubChem.
Cy3 — C31H38N2O8S2, 630.8 g/mol. Real 3D structure from PubChem.
Cy7 — C35H42N2O8S2, 682.8 g/mol. Real 3D structure from PubChem.
DiI — Lipophilic membrane dye for tracking cells, exosomes and liposomes. C59H97ClN2O4, 933.9 g/mol. Real 3D structure from PubChem.
DiO — C53H85ClN2O6, 881.7 g/mol. Real 3D structure from PubChem.
DiR — Near-infrared lipophilic dye for in-vivo imaging of nanoparticles. C63H101IN2, 1013.4 g/mol. Real 3D structure from PubChem.
Acridine orange — C17H19N3, 265.35 g/mol. Real 3D structure from PubChem.
Texas Red — C31H29ClN2O6S2, 625.2 g/mol. Real 3D structure from PubChem.
Aminolevulinic acid — C5H9NO3, 131.13 g/mol. Real 3D structure from PubChem.
Protoporphyrin IX — C34H34N4O4, 562.7 g/mol. Real 3D structure from PubChem.
Chlorin e6 — Photosensitiser for photodynamic therapy. C34H36N4O6, 596.7 g/mol. Real 3D structure from PubChem.
Verteporfin — Liposomal photosensitiser (Visudyne) for macular degeneration. Real 3D structure from PubChem.
Gadoterate — C16H24GdN4O8-, 557.63 g/mol. Real 3D structure from PubChem.
Gadobutrol — Gadolinium MRI contrast agent. C18H31GdN4O9, 604.7 g/mol. Real 3D structure from PubChem.
Iohexol — C19H26I3N3O9, 821.1 g/mol. Real 3D structure from PubChem.
FDG (fludeoxyglucose) — C6H11FO5, 182.15 g/mol. Real 3D structure from PubChem.
D-Luciferin — Substrate of firefly luciferase used for bioluminescence imaging. C11H8N2O3S2, 280.3 g/mol. Real 3D structure from PubChem.
Coelenterazine — C26H21N3O3, 423.5 g/mol. Real 3D structure from PubChem.
X-gal — C14H15BrClNO6, 408.63 g/mol. Real 3D structure from PubChem.
TMB — C16H20N2, 240.34 g/mol. Real 3D structure from PubChem.
MTT — C18H16BrN5S, 414.3 g/mol. Real 3D structure from PubChem.
Resazurin — C12H7NO4, 229.19 g/mol. Real 3D structure from PubChem.
Trypan blue — C34H24N6Na4O14S4, 960.8 g/mol. Real 3D structure from PubChem.
Crystal violet — C25H30ClN3, 408 g/mol. Real 3D structure from PubChem.
Eosin Y — C20H6Br4Na2O5, 691.9 g/mol. Real 3D structure from PubChem.
Hematoxylin — C16H14O6, 302.28 g/mol. Real 3D structure from PubChem.
Congo red — C32H22N6Na2O6S2, 696.7 g/mol. Real 3D structure from PubChem.
Thioflavin T — C17H19ClN2S, 318.9 g/mol. Real 3D structure from PubChem.
JC-1 — C25H27Cl4IN4, 652.2 g/mol. Real 3D structure from PubChem.
DCFH-DA — C24H14Cl2O7, 485.3 g/mol. Real 3D structure from PubChem.
Alexa Fluor 488 — Real 3D structure from PubChem.
Fluorescein diacetate — C24H16O7, 416.4 g/mol. Real 3D structure from PubChem.
SYTOX Green — Real 3D structure from PubChem.
Rose Bengal — C20H2Cl4I4K2O5, 1049.8 g/mol. Real 3D structure from PubChem.
IR-780 — C36H44ClIN2, 667.1 g/mol. Real 3D structure from PubChem.
IR-820 — C46H50ClN2NaO6S2, 849.5 g/mol. Real 3D structure from PubChem.
Zinc phthalocyanine — C32H16N8Zn, 577.9 g/mol. Real 3D structure from PubChem.
Fluorescein 5-isothiocyanate — Real 3D structure from PubChem.
Visudyne — Real 3D structure from PubChem.
Gadopentetic acid — Real 3D structure from PubChem.
Gadoxetic acid — Real 3D structure from PubChem.
Gadodiamide — Real 3D structure from PubChem.
Iopamidol — Real 3D structure from PubChem.
Iodixanol — Real 3D structure from PubChem.
Barium sulfate — Real 3D structure from PubChem.
Technetium Tc 99m sestamibi — Real 3D structure from PubChem.
Perfluorooctyl bromide — Real 3D structure from PubChem.
Perflutren — Real 3D structure from PubChem.
Sulfur hexafluoride — Real 3D structure from PubChem.
IRDye 800CW — Real 3D structure from PubChem.
Fluorescein sodium — Real 3D structure from PubChem.
Rhodamine 123 — Real 3D structure from PubChem.
Tetramethylrhodamine methyl ester — Real 3D structure from PubChem.
Fluo-4 — Real 3D structure from PubChem.
Fura-2 — Real 3D structure from PubChem.
DiD — Real 3D structure from PubChem.
Hoechst 33258 — Real 3D structure from PubChem.
SYBR Green I — Real 3D structure from PubChem.
BCECF — Real 3D structure from PubChem.
Pyranine — Real 3D structure from PubChem.
5-carboxyfluorescein — Real 3D structure from PubChem.
Sulforhodamine B — Real 3D structure from PubChem.
FM 1-43 — Real 3D structure from PubChem.
Laurdan — Real 3D structure from PubChem.
Prodan — Real 3D structure from PubChem.
1,6-diphenyl-1,3,5-hexatriene — Real 3D structure from PubChem.
Luminol — Real 3D structure from PubChem.
Lucigenin — Real 3D structure from PubChem.
Amplex Red — Real 3D structure from PubChem.
2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) — Real 3D structure from PubChem.
o-phenylenediamine — Real 3D structure from PubChem.
4-methylumbelliferone — Real 3D structure from PubChem.
Resorufin — Real 3D structure from PubChem.
XTT — Real 3D structure from PubChem.
Neutral red — Real 3D structure from PubChem.
Alizarin red S — Real 3D structure from PubChem.
Toluidine blue — Real 3D structure from PubChem.
Safranin O — Real 3D structure from PubChem.
Alcian blue — Real 3D structure from PubChem.
Oil Red O — Real 3D structure from PubChem.
Sudan Black B — Real 3D structure from PubChem.
3,3'-diaminobenzidine — Real 3D structure from PubChem.
Ponceau S — Real 3D structure from PubChem.
Coomassie Brilliant Blue G-250 — Real 3D structure from PubChem.
Bromophenol blue — Real 3D structure from PubChem.
Xylene cyanol — Real 3D structure from PubChem.
Phenol red — Real 3D structure from PubChem.
Bromothymol blue — Real 3D structure from PubChem.
Cy5.5 — Real 3D structure from PubChem.
Alexa Fluor 647 — Real 3D structure from PubChem.
ATTO 655 — Real 3D structure from PubChem.
5-aminolevulinic acid hydrochloride — Real 3D structure from PubChem.
Pafolacianine — Real 3D structure from PubChem.
Hexaminolevulinate — Real 3D structure from PubChem.