H-bond donor

SMARTS: [#7,#8;H1,H2,H3]

Aliases: HBD

Gatekeeper aromatic

SMARTS: [cX3]1[cX3][cX3][cX3][cX3][cX3]1

Aliases: hydrophobic aromatic

H-bond acceptor N

SMARTS: [#7;!$([NH2]);!$([NH1]);!$([NH0+1])]

Aliases: HBA-N

H-bond acceptor O

SMARTS: [#8;!$([OH1]);!$([OH2])]

Aliases: HBA-O

Metal chelator

SMARTS: [#7,#8]-[CX3]=[#7,#8]

Aliases: beta-ketoamide, metal binding

Hinge binder (C=O-NH)

SMARTS: [CX3](=O)[NH]

Hinge binder (NH-C=O)

SMARTS: [NH][CX3](=O)

Aliases: amide hinge contact

Ionizable base

SMARTS: [NX3;H1,H2;!$([N]~C=O);!$([N]~S=O)]

P-gp efflux flag

SMARTS: [NX3H0]([#6])([#6])[#6]

Aliases: P-glycoprotein

ATP mimic pyrimidine

SMARTS: c1ccncn1

Aliases: kinase scaffold

Catechol

SMARTS: Oc1ccccc1O

Aliases: 1,2-dihydroxybenzene

Sulfonamide bioisostere

SMARTS: [SX4](=O)(=O)[NX3]

Aliases: SO2NHR amide isostere

N-Methyl amide

SMARTS: [NX3;H0]([#6])[CX3](=O)

Aliases: N-MeAA backbone

Michael acceptor (extended)

SMARTS: [CX3]=[CX3][CX3](=O)

Aliases: activated olefin PAINS

Retro-amide

SMARTS: [CX3](=O)[CX4][NX3]

Michael acceptor

SMARTS: [CX3;!R]=[CX3][CX3]=O

Aliases: activated alkene, enone

β-Turn mimetic

SMARTS: [NX3][CX4][CX4][NX3]

Resorcinol

SMARTS: Oc1cccc(O)c1

Aliases: 1,3-dihydroxybenzene

Peptide backbone

SMARTS: [NX3][CX4][CX3](=O)[NX3]

Aliases: amide bond peptide

Chalcone

SMARTS: O=CC=Cc1ccccc1

Hydroquinone

SMARTS: Oc1ccc(O)cc1

Aliases: 1,4-dihydroxybenzene

Aza-Michael acceptor

SMARTS: [NX3][CX3]=[CX3]

Acrylamide

SMARTS: [CX3H1]=[CX3][CX3](=O)[NX3]

Aliases: alpha,beta-unsaturated amide, covalent warhead

Proline-like ring

SMARTS: [NX3r5]1[CX4r5][CX4r5][CX4r5][CX4r5]1

Aliases: cyclic secondary amine N

Polyol

SMARTS: [OX2H][CX4][CX4][OX2H]

Aliases: 1,2-diol, vicinal diol

Biphenyl

SMARTS: c1ccc(-c2ccccc2)cc1

Nucleoside sugar

SMARTS: [OX2r5]1[CX4r5][CX4r5][CX4r5][CX4r5]1

Aliases: furanose, ribose

Lipinski HMW fragment

SMARTS: [#6;!R;!$(C(=O))][#6;!R;!$(C(=O))][#6;!R;!$(C(=O))][#6;!R;!$(C(=O))][#6;!R]

Aliases: lipophilic chain

Pyranose sugar

SMARTS: [OX2r6]1[CX4r6][CX4r6][CX4r6][CX4r6][CX4r6]1

Aliases: glucose ring, hexose ring

PAINS — catechol

SMARTS: Oc1ccc(cc1O)[CX3]=O

Aliases: PAINS catechol

Vinyl sulfone

SMARTS: [CX3]=[CX3][SX4](=O)(=O)

α-Amino acid

SMARTS: [NX3][CX4][CX3](=O)[OX2H]

Aliases: amino acid

ATP mimic purine

SMARTS: c1ncnc2[nH]cnc12

Aliases: adenine core kinase

Boronic acid warhead

SMARTS: [BX3]([OX2H])[OX2H]

Aliases: boronic acid protease inhibitor

Salicylate

SMARTS: Oc1ccccc1C(=O)[OX2H]

Aliases: 2-hydroxybenzoate

Aldehyde warhead

SMARTS: [CX3H1](=O)[#6;!$(C(=O))]

Aliases: covalent aldehyde

Fluoroacetamide

SMARTS: FCC(=O)[NX3]

Epoxide warhead

SMARTS: [OX2r3][CX4r3][CX3](=O)

Aliases: alpha-beta-epoxy carbonyl

Stilbene

SMARTS: c1ccc(/C=C/c2ccccc2)cc1

β-Lactam

SMARTS: [NX3r4][CX3r4](=O)

Aliases: azetidinone

Quinone

SMARTS: O=C1C=CC(=O)C=C1

Chloroacetamide

SMARTS: ClCC(=O)[NX3]

Aliases: electrophilic warhead

α-Cyanoacrylamide

SMARTS: N#C[CX3]=[CX3][CX3](=O)[NX3]

Quinone alert

SMARTS: O=C1C=CC(=O)C=C1

Aliases: quinone PAINS

Nitrile warhead

SMARTS: [NX1]#[CX2][CX3](=O)[NX3]

Aliases: cyanoamide warhead

Nitroaromatic

SMARTS: [$([NX3](=O)=O),$([NX3+](=O)[O-])]c

Aliases: Ar-NO2

Thiol-reactive

SMARTS: [Cl,Br,I][CX4][CX3](=O)

Aliases: alkylating agent

Isocyanate warhead

SMARTS: [NX2]=C=O

Aldehyde (PAINS)

SMARTS: [CX3H1](=O)c

Aliases: aryl aldehyde alert

Haloamide alert

SMARTS: [Cl,Br,I][CX4][CX3](=O)[NX3]

Diacyl peroxide

SMARTS: [CX3](=O)[OX2][OX2][CX3](=O)

PAINS — rhodanine

SMARTS: O=C1CSSC(=S)N1

Aliases: PAINS rhodanine

Carbonyl

SMARTS: [CX3]=[OX1]

Aliases: C=O

Secondary amine

SMARTS: [NX3H1]([#6])[#6]

Aliases: NH

Ether

SMARTS: [OD2]([#6])[#6]

Amide

SMARTS: [CX3](=O)[NX3]

Aliases: carboxamide

Tertiary amine

SMARTS: [NX3]([#6])([#6])[#6]

Aryl ether

SMARTS: [OD2]([cX3])[#6]

Aliases: phenyl ether

Phenol

SMARTS: [OX2H][cX3]

Aliases: ArOH

Chlorine

SMARTS: [ClX1]

Aliases: Cl, chloro

Imine

SMARTS: [CX3]=[NX2]

Aliases: Schiff base

Alkene

SMARTS: [CX3]=[CX3]

Aliases: C=C, olefin

Sulfonamide

SMARTS: [SX4](=O)(=O)[NX3]

Aliases: SO2NH

Lactam

SMARTS: [CX3](=O)[NX3;R]

Alcohol

SMARTS: [OX2H][CX4]

Aliases: OH, hydroxyl

Primary amine

SMARTS: [NX3H2][#6]

Aliases: NH2

Ester

SMARTS: [CX3](=O)[OX2][#6]

Sulfide

SMARTS: [SX2D2]([#6])[#6]

Aliases: thioether

Enone

SMARTS: [CX3]=[CX3][CX3]=O

Aliases: alpha,beta-unsaturated ketone

Fluorine

SMARTS: [FX1]

Aliases: F, fluoro

Ketone

SMARTS: [#6][CX3](=O)[#6]

Bromine

SMARTS: [BrX1]

Aliases: Br, bromo

Acetal

SMARTS: [CX4]([OX2][#6])([OX2][#6])

Nitrile

SMARTS: [NX1]#[CX2]

Aliases: CN, cyano

Imide

SMARTS: [CX3](=O)[NX3][CX3](=O)

Hydrazine

SMARTS: [NX3H][NX3]

Aliases: N-N

Amidine

SMARTS: [NX3][CX3]=[NX2]

Dienophile

SMARTS: [CX3]=[CX3]~[CX3]=[CX3]

Aliases: diene

Urea

SMARTS: [NX3][CX3](=O)[NX3]

Trifluoromethyl

SMARTS: [CX4](F)(F)F

Aliases: CF3

Enol ether

SMARTS: [CX3]=[CX3][OX2]

Aliases: vinyl ether

Carboxylic acid

SMARTS: [CX3](=O)[OX2H1]

Aliases: COOH, acid

Thioamide

SMARTS: [CX3](=S)[NX3]

Carbamate

SMARTS: [NX3][CX3](=O)[OX2]

Aliases: urethane

Sulfone

SMARTS: [SX4](=O)(=O)([#6])[#6]

Aliases: SO2

Vinyl

SMARTS: [CX3H2]=[CX3]

Alkyne

SMARTS: [CX2]#[CX2]

Aliases: C#C, acetylene

Guanidine

SMARTS: [NX3][CX3](=[NX2])[NX3]

Lactone

SMARTS: [CX3](=O)[OX2;R]

Epoxide

SMARTS: [OX2r3]1[CX4r3][CX4r3]1

Aliases: oxirane

Hemiacetal

SMARTS: [CX4]([OX2H])([OX2][#6])

Dithiocarbamate

SMARTS: [NX3][CX3](=S)[SX2]

Oxime

SMARTS: [CX3]=[NX2][OX2H]

Phosphate

SMARTS: [PX4](=O)([OX2])[OX2]

Aliases: PO4

Difluoromethyl

SMARTS: [CX4H1](F)F

Aliases: CHF2

Disulfide

SMARTS: [SX2D2][SX2D2]

Aliases: S-S

Thioester

SMARTS: [CX3](=O)[SX2][#6]

Aliases: thiolester

Sulfonic acid

SMARTS: [SX4](=O)(=O)[OX2H]

Aliases: SO3H

Phosphonate

SMARTS: [PX4](=O)([OX2])[#6]

Sulfate

SMARTS: [SX4](=O)(=O)([OX2])[OX2H]

Aliases: OSO3H

Sulfinyl

SMARTS: [SX3](=O)

Thiol

SMARTS: [SX2H]

Aliases: SH, mercapto

Iodine

SMARTS: [IX1]

Aliases: I, iodo

Perfluoroalkyl

SMARTS: [CX4](F)(F)[CX4]

Azo

SMARTS: [#6][NX2]=[NX2][#6]

Aliases: N=N

Anhydride

SMARTS: [CX3](=O)O[CX3](=O)

Peroxide

SMARTS: [OX2D2][OX2D2]

Aldehyde

SMARTS: [CX3H1](=O)[#6]

Aliases: CHO

Boronic acid

SMARTS: [BX3]([OX2H])[OX2H]

Aliases: B(OH)2

Sulfoxide

SMARTS: [SX3](=O)([#6])[#6]

Aliases: S=O

α-Haloketone

SMARTS: [F,Cl,Br,I][CX4][CX3](=O)

Hydroxamic acid

SMARTS: [CX3](=O)[NX3][OX2H]

Hydrazone

SMARTS: [NX2]=[NX3H]

Phosphoramide

SMARTS: [PX4](=O)([NX3])[OX2]

Silyl ether

SMARTS: [SiX4][OX2][#6]

Aliases: TBS, TMS

Nitro

SMARTS: [$([NX3](=O)=O),$([NX3+](=O)[O-])]

Aliases: NO2

Acyl halide

SMARTS: [CX3](=O)[F,Cl,Br,I]

Nitroso

SMARTS: [NX2]=[OX1]

Aliases: N=O

Sulfonyl chloride

SMARTS: [SX4](=O)(=O)[Cl]

Aliases: SO2Cl

Azide

SMARTS: [NX1]=[NX2]=[NX1]

Aliases: N3

Boronate ester

SMARTS: [BX3]([OX2][#6])[OX2][#6]

Sulfamate

SMARTS: [NX3][SX4](=O)(=O)[OX2]

Carbonate

SMARTS: [OX2][CX3](=O)[OX2]

Isocyanate

SMARTS: [NX2]=C=O

Aliases: NCO

Isothiocyanate

SMARTS: [NX2]=C=S

Aliases: NCS

Phosphine oxide

SMARTS: [PX4](=O)([#6])([#6])[#6]

Semicarbazone

SMARTS: [NX3H][CX3](=O)[NX2]=[CX3]

Thiosemicarbazone

SMARTS: [NX3H][CX3](=S)[NX2]=[CX3]

Phosphine

SMARTS: [PX3]([#6])([#6])[#6]

Diazo

SMARTS: [CX3]=[NX2+]=[NX1-]

Aliases: diazomethane

Diazonium

SMARTS: [#6][N+]#N

Isonitrile

SMARTS: [NX1+]#[CX2-]

Aliases: NC, isocyanide

Allene

SMARTS: [CX2](=[CX2])=[CX2]

Aliases: propadiene

Benzene

SMARTS: c1ccccc1

Aliases: arene, phenyl

Cyclohexane

SMARTS: C1CCCCC1

Pyrimidine

SMARTS: c1ccncn1

Pyridine

SMARTS: c1ccncc1

Pipecolinyl ring

SMARTS: [N]1CCCCC1

Aliases: N-methylpiperidine, pipecolinyl

Thiophene

SMARTS: c1ccsc1

Quinoline

SMARTS: c1ccc2ncccc2c1

Thiazole

SMARTS: c1cscn1

Imidazole

SMARTS: c1cnc[nH]1

Pyrrole

SMARTS: [nH]1cccc1

Aliases: 1H-pyrrole

Indole

SMARTS: c1ccc2[nH]ccc2c1

Isoindole

SMARTS: c1ccc2[nH]ccc2c1

Furan

SMARTS: c1ccoc1

Cyclopentane

SMARTS: C1CCCC1

Naphthalene

SMARTS: c1ccc2ccccc2c1

Benzimidazole

SMARTS: c1ccc2nc[nH]c2c1

Piperidine

SMARTS: [NH]1CCCCC1

Pyrazole

SMARTS: c1cc[nH]n1

Chromane

SMARTS: O1CCCc2ccccc21

Aliases: 3,4-dihydro-2H-chromene

Chromene

SMARTS: c1ccc2c(c1)OCCC2

Aliases: 2H-chromene

Piperazine

SMARTS: [NH]1CCNCC1

Hexahydropyrimidine

SMARTS: [NH]1CCNCC1

Tetrahydropyrimidine

SMARTS: [NH]1CCNCC1

Tetrahydrofuran

SMARTS: O1CCCC1

Aliases: THF

Pyrazine

SMARTS: c1cnccn1

Benzodioxane

SMARTS: c1cc2OCCOc2cc1

Azepane

SMARTS: [NH]1CCCCCC1

Benzodioxole

SMARTS: c1cc2OCOc2cc1

Aliases: MDP, methylenedioxyphenyl

Pyridazine

SMARTS: c1ccnnc1

Pyrrolidine

SMARTS: [NH]1CCCC1

Cyclopropane

SMARTS: C1CC1

Isoxazole

SMARTS: c1ccno1

1,2,4-Oxadiazole

SMARTS: c1conc1

Benzothiazole

SMARTS: c1ccc2scnc2c1

Tetrahydropyran

SMARTS: O1CCCCC1

Aliases: THP

1,2,4-Triazole

SMARTS: c1nc[nH]n1

Benzofuran

SMARTS: c1ccc2occc2c1

Oxadiazole

SMARTS: c1nnco1

1,3,4-Oxadiazole

SMARTS: c1nnco1

Isoquinoline

SMARTS: c1ccc2cnccc2c1

Oxirane

SMARTS: O1CC1

Aliases: epoxide ring, ethylene oxide

Cinnoline

SMARTS: c1ccc2cnncc2c1

Imidazo[1,2-a]pyridine

SMARTS: c1ccn2ccnc2c1

Decalin

SMARTS: C1CCC2CCCCC2C1

Aliases: decahydronaphthalene

Oxazole

SMARTS: c1cocn1

Indoline

SMARTS: [NH]1CCc2ccccc21

Aliases: 2,3-dihydroindole

Pyrazolo[1,5-a]pyridine

SMARTS: c1ccn2cccnc2c1

Thiolane

SMARTS: S1CCCC1

Aliases: tetrahydrothiophene

Coumarin

SMARTS: O=c1ccc2ccccc2o1

Aliases: 2H-chromen-2-one, chromenone

Benzomorpholine

SMARTS: [NH]1CCOc2ccccc21

Imidazolidine

SMARTS: [NH]1CCNC1

Triazine

SMARTS: c1ncncn1

Aliases: s-triazine

Flavone

SMARTS: O=c1cc(-c2ccccc2)oc2ccccc12

Spirocycle

SMARTS: [CX4r]([R1])([R1])([R2])[R2]

Aliases: spiro

Quinazoline

SMARTS: c1nc2ccccc2nc1

Quinoxaline

SMARTS: c1cnc2ccccc2n1

Benzoxazole

SMARTS: c1ccc2ocnc2c1

Benzothiophene

SMARTS: c1ccc2sccc2c1

Adamantane

SMARTS: C1C2CC3CC1CC(C2)C3

Cyclobutane

SMARTS: C1CCC1

Dithiolane

SMARTS: S1CCCS1

Morpholine

SMARTS: [NH]1CCOCC1

Dioxolane

SMARTS: O1COCC1

Purine

SMARTS: c1ncnc2[nH]cnc12

Indazole

SMARTS: c1ccc2[nH]ncc2c1

Hypoxanthine

SMARTS: O=c1[nH]cnc2ncnc12

Adenine

SMARTS: Nc1ncnc2[nH]cnc12

Uracil

SMARTS: O=c1cc[nH]c(=O)[nH]1

Phenothiazine

SMARTS: c1ccc2Nc3ccccc3Sc2c1

Chromanone

SMARTS: O=C1CCOc2ccccc21

Aliases: 3,4-dihydrocoumarin

Dihydrobenzofuran

SMARTS: O1CCc2ccccc21

Aliases: 2,3-dihydrobenzofuran

Pyrazolidine

SMARTS: [NH]1CCCN1

Cycloheptane

SMARTS: C1CCCCCC1

Cytosine

SMARTS: Nc1ccnc(=O)[nH]1

Xanthene

SMARTS: c1ccc2c(c1)Cc1ccccc1O2

Dioxane

SMARTS: O1CCOCC1

Naphthyridine

SMARTS: c1cnc2ncccc2c1

Anthracene

SMARTS: c1ccc2cc3ccccc3cc2c1

Phenanthrene

SMARTS: c1ccc2c(c1)ccc1ccccc12

Tetrazole

SMARTS: c1nn[nH]n1

Fluorene

SMARTS: c1ccc2cc3ccccc3cc2c1

Thiazolidine

SMARTS: [NH]1CCSC1

Oxepane

SMARTS: O1CCCCCC1

Isothiazole

SMARTS: c1ccns1

Phthalazine

SMARTS: c1ccc2nnccc2c1

Tetrahydroisoquinoline

SMARTS: [NH]1CCc2ccccc2CC1

Aliases: 1,2,3,4-THIQ

Isoindolinone

SMARTS: O=C1CNc2ccccc21

Aliases: isoindolin-1-one

Oxindole

SMARTS: O=C1CNc2ccccc12

Aliases: indolin-2-one, oxindole

Dibenzofuran

SMARTS: c1ccc2oc3ccccc3c2c1

Thiazine

SMARTS: C1CSCCN1

Benzotriazole

SMARTS: c1ccc2[nH]nnc2c1

Guanine

SMARTS: Nc1nc2[nH]cnc2c(=O)[nH]1

1,2,3-Triazole

SMARTS: c1cn[nH]n1

Aliases: triazole

Acridine

SMARTS: c1ccc2nc3ccccc3cc2c1

Xanthine

SMARTS: O=c1[nH]cnc2[nH]c(=O)[nH]c12

Benzisothiazole

SMARTS: c1ccc2nscc2c1

Aliases: 1,2-benzisothiazole

Benzisoxazole

SMARTS: c1ccc2nocc2c1

Aliases: 1,2-benzisoxazole

Carbazole

SMARTS: c1ccc2[nH]c3ccccc3c2c1

Tetrahydroquinoline

SMARTS: [NH]1CCCc2cccnc21

Aliases: 1,2,3,4-THQ

Phenanthridine

SMARTS: c1ccc2nc3ccccc3cc2c1

Phenoxazine

SMARTS: c1ccc2Nc3ccccc3Oc2c1

Pteridine

SMARTS: c1cnc2nccnc2n1

Steroid core

SMARTS: C1CC2CCC3CCCC4CCCC1C4C3C2

Aliases: gonane, perhydrophenanthrene

Thymine

SMARTS: O=c1c(C)c[nH]c(=O)[nH]1

Furanopyrimidine

SMARTS: c1cnc2occc2n1

Pyrazolo[1,5-a]pyrimidine

SMARTS: c1cnc2ccnn2n1

Thienopyrimidine

SMARTS: c1cnc2sccc2n1

Thiomorpholine

SMARTS: [NH]1CCSCC1

1,3,4-Thiadiazole

SMARTS: c1nnsc1

Azetidine

SMARTS: [NH]1CCC1

Aziridine

SMARTS: [NH]1CC1

Aliases: ethylenimine

Tetrazine

SMARTS: c1nnncn1

Aliases: 1,2,4,5-tetrazine

Thiadiazole

SMARTS: c1nns[nH]1

Xanthone

SMARTS: O=c1oc2ccccc2c2ccccc12

1,2,5-Oxadiazole

SMARTS: c1noc[nH]1

Aliases: furazan

Dibenzothiophene

SMARTS: c1ccc2sc3ccccc3c2c1

Oxazine

SMARTS: c1cocc[nH]1

Oxazolidine

SMARTS: [NH]1CCOC1

Oxetane

SMARTS: O1CCC1

Dihydropyridine

SMARTS: [NH]1CC=CCC1

Aliases: DHP

Diazepane

SMARTS: [NH]1CCNCCCC1

Tetrahydrothiopyran

SMARTS: S1CCCCC1

Aliases: thiane

Thietane

SMARTS: S1CCC1

Thiirane

SMARTS: S1CC1

Aliases: episulfide

Trioxane

SMARTS: O1COCOC1

Trithiolane

SMARTS: S1CSCS1