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Functional Groups
81
Ring Systems
126
Bio Motifs
52
Carbonyls
16
â–¾
Carbonyl
Aldehyde
Amide
Carboxylic acid
Ketone
Ester
Lactam
Lactone
Acyl halide
Urea
Anhydride
Carbamate
Imide
Thioester
Carbonate
Dithiocarbamate
Amines & N-groups
22
â–¾
Primary amine
Secondary amine
Nitrile
Nitro
Tertiary amine
Nitroso
Amidine
Azide
Guanidine
Azo
Hydrazine
Hydrazone
Hydroxamic acid
Imine
Oxime
Isocyanate
Isothiocyanate
Semicarbazone
Thiosemicarbazone
Diazo
Diazonium
Isonitrile
Hydroxy & Ether
9
â–¾
Alcohol
Phenol
Epoxide
Aryl ether
Ether
Enol ether
Acetal
Hemiacetal
Peroxide
Halogens
8
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Trifluoromethyl
Bromine
Chlorine
Fluorine
Difluoromethyl
Iodine
Perfluoroalkyl
α-Haloketone
Sulfur
12
â–¾
Sulfonamide
Thiol
Sulfone
Sulfonic acid
Sulfoxide
Sulfonyl chloride
Sulfide
Sulfamate
Sulfate
Disulfide
Sulfinyl
Thioamide
P & B
8
â–¾
Boronic acid
Boronate ester
Phosphate
Phosphonate
Phosphoramide
Phosphine oxide
Silyl ether
Phosphine
Unsaturated C
6
â–¾
Enone
Alkene
Alkyne
Vinyl
Dienophile
Allene
5-membered: N
6
â–¾
Imidazole
Pyrazole
Pyrrole
1,2,3-Triazole
1,2,4-Triazole
Tetrazole
5-membered: O/S
14
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Furan
Thiophene
Isoxazole
Oxazole
Thiazole
Isothiazole
Oxadiazole
1,2,4-Oxadiazole
1,3,4-Oxadiazole
1,3,4-Thiadiazole
Thiadiazole
1,2,5-Oxadiazole
Dithiolane
Trithiolane
6-membered aromatic
9
â–¾
Benzene
Pyridine
Pyrimidine
Pyrazine
Pyridazine
Triazine
Tetrazine
Oxazine
Thiazine
Saturated N rings
17
â–¾
Morpholine
Piperazine
Piperidine
Pyrrolidine
Thiomorpholine
Azetidine
Aziridine
Imidazolidine
Oxazolidine
Pyrazolidine
Thiazolidine
Pipecolinyl ring
Azepane
Dihydropyridine
Hexahydropyrimidine
Tetrahydropyrimidine
Diazepane
Saturated O/S rings
12
â–¾
Tetrahydrofuran
Tetrahydropyran
Oxirane
Oxetane
Dioxane
Dioxolane
Thiolane
Tetrahydrothiopyran
Oxepane
Thietane
Thiirane
Trioxane
Benzo-fused
45
â–¾
Indole
Quinoline
Benzimidazole
Indazole
Isoquinoline
Quinazoline
Quinoxaline
Benzothiazole
Benzoxazole
Benzofuran
Benzothiophene
Benzotriazole
Naphthalene
Coumarin
Acridine
Benzisothiazole
Benzisoxazole
Carbazole
Indoline
Isoindole
Naphthyridine
Phthalazine
Tetrahydroisoquinoline
Tetrahydroquinoline
Anthracene
Cinnoline
Flavone
Phenanthrene
Phenanthridine
Phenothiazine
Phenoxazine
Isoindolinone
Oxindole
Benzodioxole
Benzodioxane
Benzomorpholine
Chromane
Chromanone
Chromene
Dihydrobenzofuran
Xanthone
Dibenzofuran
Dibenzothiophene
Fluorene
Xanthene
Purines
14
â–¾
Purine
Adenine
Guanine
Xanthine
Cytosine
Hypoxanthine
Uracil
Imidazo[1,2-a]pyridine
Pteridine
Pyrazolo[1,5-a]pyridine
Thymine
Furanopyrimidine
Pyrazolo[1,5-a]pyrimidine
Thienopyrimidine
Carbocycles
9
â–¾
Steroid core
Cyclohexane
Cyclopropane
Cyclopentane
Decalin
Adamantane
Cyclobutane
Spirocycle
Cycloheptane
Reactive warheads
16
â–¾
β-Lactam
Acrylamide
Quinone
Michael acceptor
Vinyl sulfone
Boronic acid warhead
Chloroacetamide
α-Cyanoacrylamide
Aldehyde warhead
Epoxide warhead
Fluoroacetamide
Nitrile warhead
Thiol-reactive
Aza-Michael acceptor
Isocyanate warhead
Diacyl peroxide
Natural product motifs
11
â–¾
α-Amino acid
Catechol
Biphenyl
Salicylate
Hydroquinone
Resorcinol
Chalcone
Nucleoside sugar
Pyranose sugar
Stilbene
Polyol
ADME flags
6
â–¾
H-bond acceptor N
H-bond acceptor O
H-bond donor
Ionizable base
Lipinski HMW fragment
P-gp efflux flag
Kinase pharmacophores
5
â–¾
ATP mimic purine
ATP mimic pyrimidine
Hinge binder (C=O-NH)
Hinge binder (NH-C=O)
Gatekeeper aromatic
PAINS / toxic alerts
8
â–¾
Quinone alert
Nitroaromatic
Aldehyde (PAINS)
Haloamide alert
Michael acceptor (extended)
Metal chelator
PAINS — catechol
PAINS — rhodanine
Peptide mimetics
6
â–¾
Peptide backbone
Proline-like ring
Sulfonamide bioisostere
N-Methyl amide
β-Turn mimetic
Retro-amide
Compounds
⬡
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