BioLibrary › Molecules
Molecules: 4,581 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.
- Anticancer drugs 138 models
Doxorubicin · Daunorubicin · Epirubicin · Idarubicin · Paclitaxel · Docetaxel · Cabazitaxel · Cisplatin …
- Natural compounds 39 models
Curcumin · Resveratrol · Quercetin · Berberine · Artemisinin · EGCG (epigallocatechin gallate) · Capsaicin · Piperine …
- Anti-infectives 112 models
Benzylpenicillin · Amoxicillin · Ampicillin · Ceftriaxone · Meropenem · Ciprofloxacin · Levofloxacin · Tetracycline …
- Common medicines 79 models
Aspirin · Ibuprofen · Paracetamol (acetaminophen) · Naproxen · Diclofenac · Celecoxib · Indomethacin · Morphine …
- Lipids & surfactants 86 models
DSPC · DPPC · DOPC · POPC · DOPE · DMPC · DOTAP · DOTMA …
- Polymers & crosslinkers 105 models
Lactic acid · Glycolic acid · Lactide · Glycolide · Caprolactone · Ethylene glycol · Tetraethylene glycol · Acrylic acid …
- Dyes & imaging agents 111 models
Fluorescein · FITC · Rhodamine B · Rhodamine 6G · TRITC · DAPI · Hoechst 33342 · Propidium iodide …
- Biomolecules & metabolites 178 models
Glycine · L-alanine · L-valine · L-leucine · L-isoleucine · L-proline · L-phenylalanine · L-tryptophan …
- Nucleic-acid chemistry 25 models
Pseudouridine (Ψ) · N1-Methylpseudouridine (m1Ψ) · 5-methylcytidine · 2'-O-methyladenosine · 2'-fluoro-2'-deoxyuridine · 7-Methylguanosine (m7G, cap) · N6-Methyladenosine (m6A) · Inosine …
- Solvents, gases & buffers 43 models
Water · Oxygen · Carbon dioxide · Nitrogen · Nitric oxide · Carbon monoxide · Hydrogen sulfide · Hydrogen peroxide …
- Nervous system drugs 61 models
Paroxetine · Escitalopram · Venlafaxine · Duloxetine · Bupropion · Mirtazapine · Trazodone · Lithium carbonate …
- Cardiovascular & metabolic drugs 59 models
Ezetimibe · Fenofibrate · Gemfibrozil · Niacin · Dapagliflozin · Empagliflozin · Canagliflozin · Pioglitazone …
- Hormones, reproductive & skin drugs 50 models
Misoprostol · Mifepristone · Clomiphene · Medroxyprogesterone acetate · Levonorgestrel · Ethinyl estradiol · Norethisterone · Testosterone undecanoate …
- Toxins & natural alkaloids 55 models
Cocaine · Scopolamine · Quinine · Strychnine · Tetrodotoxin · Saxitoxin · Aflatoxin B1 · Ochratoxin A …
- Sugars & glycans 35 models
Cellobiose · Raffinose · Stachyose · N-acetylmuramic acid · Rhamnose · Xylose · Arabinose · Xylitol …
- Targeting ligands & carriers 26 models
Cyclo(RGDfK) · Arginylglycylaspartic acid · Glycyrrhetinic acid · Anisamide · Lactobionic acid · Methyltriphenylphosphonium bromide · Dequalinium · Cholic acid …
- Inorganic & MOF precursors 51 models
2-methylimidazole · Terephthalic acid · Trimesic acid · Zirconium tetrachloride · Imidazole · Biphenyl-4,4'-dicarboxylic acid · 4,4'-bipyridine · Zinc nitrate …
- Approved drugs · Nervous system 263 models
Mianserin · Imipramine · Carbachol · Clomipramine · Trifluoperazine · Sulpiride · Thiopental · Cyclobarbital …
- Approved drugs · Cardiovascular 146 models
Prazosin · Isosorbide dinitrate · Indapamide · Mecamylamine · Practolol · Labetalol · Spirapril · Isoproterenol …
- Approved drugs · Anti-infectives 137 models
Sulbactam · Norfloxacin · Penicillin g · Trovafloxacin · Gemifloxacin · Sulfadiazine · Sulfamethazine · Sulfisoxazole …
- Approved drugs · Digestive & metabolic 127 models
Troglitazone · Olsalazine · Cimetidine · Tolrestat · Glyburide · Lansoprazole · Pirenzepine · Chlorpropamide …
- Approved drugs · Cancer & immunomodulators 94 models
Mechlorethamine · Amsacrine · Aminoglutethimide · Plerixafor · Tegafur · Anagrelide · Flutamide · Omacetaxine mepesuccinate …
- Approved drugs · Respiratory 87 models
Cromolyn · Chlorpheniramine · Pyrilamine · Cyproheptadine · Ketotifen · Terfenadine · Acetylcysteine · Zafirlukast …
- Approved drugs · Dermatology 78 models
Mafenide · Sulfanilamide · Sulfathiazole · Sulfamerazine · Etretinate · Podofilox · Hexachlorophene · Clioquinol …
- Approved drugs · Urology & sex hormones 70 models
Diethylstilbestrol · Bromocriptine · Miconazole · Benzydamine · Dinoprostone · Terazosin · Silodosin · Alfuzosin …
- Approved drugs · Musculoskeletal 69 models
Etoricoxib · Meclofenamic acid · Piroxicam · Phenylbutazone · Flurbiprofen · Sulindac · Ketoprofen · Indoprofen …
- Approved drugs · Various (diagnostics, antidotes) 58 models
Flumazenil · Aminohippuric acid · Macimorelin · Tolbutamide · Iopanoic acid · Metyrapone · Iophendylate · Mesna …
- Approved drugs · Eye & ear 50 models
Dichlorphenamide · Methazolamide · Betaxolol · Gatifloxacin · Sulfacetamide · Emedastine · Apraclonidine · Guanethidine …
- Approved drugs · Blood & haematology 39 models
Melagatran · Iloprost · Menadione · Phenindione · Fluindione · Cilostazol · Ticlopidine · Nitrofurazone …
- Approved drugs · Antiparasitic 34 models
Pyrimethamine · Quinacrine · Benznidazole · Lindane · Trimetrexate · Miltefosine · Amodiaquine · Diethylcarbamazine …
- Approved drugs · Hormones (systemic) 19 models
Methylprednisolone · Levoketoconazole · Triamcinolone · Methimazole · Propylthiouracil · Carbimazole · Rimexolone · Paricalcitol …
- Approved drugs · Other approved drugs 361 models
Ethoxzolamide · Guanabenz · Thiamylal · Butabarbital · Butalbital · Pentamidine · Hexestrol · Zileuton …
- Alkaloids (ChEBI) 108 models
Fangchinoline · Tetramethylpyrazine · Taxine B · 3,4-dimethoxyphenylethylamine · 1,3,7,9-tetramethyluric acid · Norbaeocystin · (-)-voacangine · Caracurine VII …
- Flavonoids & polyphenols (ChEBI) 132 models
Wogonin · Quercetin 3,4'-di-O-beta-D-glucoside · Pelargonin · Rhamnacene · 7,8-dihydroxyflavone · 5-hydroxy-3,3',4',7-tetramethoxyflavone · 7-O-methylmyricetin · 3,4'-dimethylkaempferol …
- Terpenoids & essential oils (ChEBI) 118 models
Deoxynivalenol · Beta-cryptoxanthin · Beta-thujaplicin · Triptofordin C 2 · Triptolidenol · Spathulenol · Beta-terpineol · Alpha-cadinol …
- Steroids & sterols (ChEBI) 106 models
20-hydroxycholesterol · Androsta-1,4,6-triene-3,17-dione · Muricholic acids · 4-methoxyestrone · Estetrol · Andrastin A · Bolandiol · Marinobufagenin …
- Amino acids & derivatives (ChEBI) 86 models
3,3',5'-triiodo-L-thyronine · L-homocysteic acid · 6-diazo-5-oxo-L-norleucine · L,L-homocystine · (2S)-2-amino-4-phosphonobutanoic acid · Sarcosine · Tabtoxinine beta-lactam · L-homoserine …
- Fatty acids (ChEBI) 54 models
2-hydroxybutyric acid · 3-hydroxydecanoic acid · (Z)-icos-13-enoic acid · Protectin D1 · 3-hydroxypentanoic acid · (2E)-3-methylhex-2-enoic acid · Leukotriene A4 · Hexadecanoic acid …
- Monosaccharides & sugars (ChEBI) 14 models
Aldose · Dihydroxyacetone · Aldehydo-L-rhamnose · 1,5-anhydro-D-glucitol · Sedoheptulose · L-fucopyranose · D-psicose · D-erythrose …
- Nucleosides (ChEBI) 17 models
Blasticidin S · S-adenosylmethioninamine · Gougerotin · 2'-deoxycytidine · 2'-deoxyuridine · Nucleocidin · 2'-deoxyguanosine · 2'-deoxyadenosine …
- Nucleotides & cofactors (ChEBI) 23 models
Adenosine 5'-monophosphate · DADP · 2'-deoxyguanosine 5'-monophosphate · CDP-choline · Uridine 5'-monophosphate · DTMP · IMP · Guanosine 5'-monophosphate …
- Phospholipids (ChEBI) 457 models
Isopentenyl diphosphate · Choline alfoscerate · Sphingosine 1-phosphate · 2-O-acetyl-1-O-hexadecyl-sn-glycero-3-phosphocholine · 2-O-acetyl-1-O-octadecyl-sn-glycero-3-phosphocholine · Perifosine · Eritoran · 1,2-dihexadecanoyl-sn-glycero-3-phosphocholine …
- Polyketides (ChEBI) 43 models
Visnagin · Flurithromycin · Amrubicin · Spectinabilin · Pyoluteorin · Fostriecin · Macrocin · Tylosin …
- Phenylpropanoids (ChEBI) 56 models
Wighteone · Ethyl trans-caffeate · Acteoside · Theaflavin · Benzyl cinnamate · Trans-sinapic acid · Scopolin · Coniferyl aldehyde …
- Porphyrins & tetrapyrroles (ChEBI) 15 models
Protoporphyrin · Copper(II) phthalocyanine · Protochlorophyllide · Bilirubin IXalpha · Cobamamide · Hydroxocobalamin · Coenzyme F430 · Siroheme …
- Peptides (ChEBI) 86 models
Beta-endorphin · Pneumocandin B0 · Lugdunin · Taltirelin · Cefbuperazone · Demoxytocin · Afamelanotide · Tetragastrin …
- Quinones (ChEBI) 26 models
Tetrahydroxy-1,4-benzoquinone · Atromentin · Acenaphthoquinone · 1,4-benzoquinone · L-dopaquinone · Alizarin · 1,2-benzoquinone · Pyrroloquinoline quinone …
- Organic acids (metabolism) (ChEBI) 234 models
Xanthurenic acid · m-toluic acid · Alisertib · Phosphonoformic acid · 3-bromopyruvic acid · Cefcapene · Cefatrizine · Cefazedone …
- Purines & pyrimidines (ChEBI) 28 models
Acetoacetyl-CoA · Isobutyryl-CoA · Isovaleryl-CoA · Trans-3-methylglutaconyl-CoA · Malonyl-CoA · Octanoyl-CoA · Phenylacetyl-CoA · Propionyl-CoA …
- Indoles (ChEBI) 29 models
Luzindole · N-arachidonoylserotonin · 1-(5-fluoropentyl)-3-(2-iodobenzoyl)indole · 1-(1-methylindol-5-yl)-3-(3-methyl-1,2-thiazol-5-yl)urea · LY-310762 · (2S)-1-(6-chloro-5-fluoroindol-1-yl)-propan-2-amine · Brivanib alaninate · N-acetylserotonin …
- Glycosides (ChEBI) 24 models
Benzoyl-beta-D-glucoside · 1-O-galloyl-beta-D-glucose · Coniferin · Mycothiol · (R)-amygdalin · Kanamycin A · Salicin · Hydroquinone O-beta-D-glucopyranoside …
Simple molecules 9
- Water (H₂O) — The solvent of life: one oxygen and two hydrogens at a 104.5° angle. (≈ 0.28 nm)
- Oxygen (O₂) — Two oxygen atoms joined by a double bond; used in cellular respiration.
- Carbon dioxide (CO₂) — A straight molecule: carbon double-bonded to two oxygens. Waste of respiration, food of photosynthesis.
- Nitrogen (N₂) — Two nitrogens held by a very strong triple bond — 78% of air.
- Methane (CH₄) — A carbon with four hydrogens arranged as a tetrahedron.
- Ammonia (NH₃) — A nitrogen with three hydrogens in a pyramid; a waste product of protein breakdown.
- Ethanol — Two carbons and a hydroxyl group — made by yeast during fermentation.
- Urea — How mammals get rid of nitrogen: a carbonyl flanked by two amine groups.
- Benzene ring — A flat ring of six carbons with alternating double bonds — the core of many biomolecules.
Sugars & fats 2
- Glucose — The six-carbon sugar cells burn for energy, shown as its ring (β-D-glucopyranose). (≈ 0.9 nm)
- Cholesterol — Four fused rings and a hydrocarbon tail; stiffens animal cell membranes.
Signalling molecules 2
- Dopamine — A neurotransmitter of reward and movement: a catechol ring with an amine tail.
- Caffeine — A purine with three methyl groups; blocks adenosine receptors to keep you awake.
Nucleotides 7
- Adenine (A) — A purine base; pairs with thymine in DNA and uracil in RNA.
- Guanine (G) — A purine base; pairs with cytosine through three hydrogen bonds.
- Cytosine (C) — A pyrimidine base; pairs with guanine.
- Thymine (T) — A pyrimidine base found only in DNA; pairs with adenine.
- Uracil (U) — The RNA version of thymine; pairs with adenine.
- Nucleotide — The building block of DNA and RNA: a base, a sugar and a phosphate. Choose the base, sugar and number of phosphates.
- ATP — Adenosine triphosphate, the energy currency of the cell. Lower the phosphates to get ADP or AMP.
Amino acids 1
- Amino acid — Every amino acid has the same backbone (amine, α-carbon, carboxyl) and a different side chain. Pick one of nine.
Ions & minerals 2
- Ion — A single charged atom. Sodium and potassium drive nerve signals; calcium triggers muscle contraction.
- Salt crystal (NaCl) — Sodium and chloride ions stacked in a cubic lattice. In water the ions separate.
Look up any molecule 1
- Any molecule (PubChem) — Type the name (or PubChem CID) of any of 100+ million compounds and its real 3D structure is downloaded from PubChem.
Oligosaccharides & glycans (ChEBI) 7
- Sophorose — oligosaccharides & glycan — a natural product or metabolite. C12H22O11, 342.3 g/mol. Real 3D structure from PubChem.
- Tetragalacturonic acid hydroxymethylester — oligosaccharides & glycan — a natural product or metabolite. C28H42O29, 842.62 g/mol. Real 3D structure from PubChem.
- Sambubiose — oligosaccharides & glycan — a natural product or metabolite. C11H20O10, 312.27 g/mol. Real 3D structure from PubChem.
- Alpha,alpha-trehalose — oligosaccharides & glycan — a natural product or metabolite. C12H22O11, 342.3 g/mol. Real 3D structure from PubChem.
- Rutinose — oligosaccharides & glycan — a natural product or metabolite. C12H22O10, 326.3 g/mol. Real 3D structure from PubChem.
- Melezitose — oligosaccharides & glycan — a natural product or metabolite. C18H32O16, 504.44 g/mol. Real 3D structure from PubChem.
- Alpha-L-rhamnopyranosyl-(1->2)-beta-D-glucopyranose — oligosaccharides & glycan — a natural product or metabolite. C12H22O10, 326.3 g/mol. Real 3D structure from PubChem.
Sphingolipids (ChEBI) 5
- Psychosine — sphingolipid — a natural product or metabolite. C24H47NO7, 461.64 g/mol. Real 3D structure from PubChem.
- Ganglioside GM2 (18:0) — sphingolipid — a natural product or metabolite. C67H121N3O26, 1384.7 g/mol. Real 3D structure from PubChem.
- Ganglioside GM1 — sphingolipid — a natural product or metabolite. C73H131N3O31, 1546.84 g/mol. Real 3D structure from PubChem.
- N,N-dimethylsphingosine — sphingolipid — a natural product or metabolite. C20H41NO2, 327.55 g/mol. Real 3D structure from PubChem.
- Ganglioside GM2 (d18:1/26:0) — sphingolipid — a natural product or metabolite. C75H137N3O26, 1496.92 g/mol. Real 3D structure from PubChem.
Prostaglandins & eicosanoids (ChEBI) 4
- Prostaglandin E1 — prostaglandins & eicosanoid — a natural product or metabolite. C20H34O5, 354.49 g/mol. Real 3D structure from PubChem.
- Prostaglandin D2 — prostaglandins & eicosanoid — a natural product or metabolite. C20H32O5, 352.47 g/mol. Real 3D structure from PubChem.
- Leukotriene C4 — prostaglandins & eicosanoid — a natural product or metabolite. C30H47N3O9S, 625.78 g/mol. Real 3D structure from PubChem.
- Thromboxane B2 — prostaglandins & eicosanoid — a natural product or metabolite. C20H34O6, 370.49 g/mol. Real 3D structure from PubChem.