SMARTS search

SureChEMBL also accept SMARTS input. Here is a use of how they can be used.

Structural alerts or "toxicophores" are substructures found in chemicals that are highly correlated with undesirable properties typically associated with human or environmental toxicity. A number of studies over the past 20 years have provided descriptions of individual chemical substructures associated with particular pharmacological endpoints, typically in the format of a Daylight SMARTS description. Moreover when such substructures are used to filter medicinally unfriendly compounds out of the drug discovery pipeline, a significant reduction in compound failure rates in the clinic has been observed. For a comprehensive and freely accessible source of structural alerts please go to the OCHEM toxalerts database.

Below are the SMARTS descriptions used by SureChEMBL that would indicate whether a compound would match one or more structural alerts and hence considered to have a MedChem unfriendly status.

Chemical_Group	SMARTS
2,2-dimethyl-4,5-dicarboxy-dithiole	C1(C)(C)SC(C(=O)O)=C(C(=O)O)S1
2,3,4_trihydroxyphenyl	c([OH])c([OH])c([OH])
2,3,5_trihydroxyphenyl	c([OH])c([OH])cc([OH])
acid_anhydrides	C(=O)OC(=O)
acid_halides	[S,C](=[O,S])[F,Br,Cl,I]
Acridine	c1c2cc4ccccc4nc2ccc1
Active_Phosphate	P(=S)([OH1,O$(O[#6])])([OH1,O$(O[#6])])[S,O]
acyl_cyanide	C(=O)-C#N
Adjacent_Ring_Double_Bonds	[*;R]=[*;R]=[*;R]
Aldehyde	[#6][C!H0]=O
Aliphatic_Triflate	COS(=O)(=O)C(F)(F)F
AlkylEnamine	[C;H1$(C([#6;!$(C=O)])),H0$(C([#6;!$(C=O)])[#6;!$(C=O)])]=[CH1]!@N([#6;!$(C(=O))])[#6;!$(C(=O))]
Allene	*=C=*
Alpha_Halo_Carbonyl	[C;!$(C[N])](=O)!@[C;h1,h2;H1,H2][F,Cl,Br,I]
amidotetrazole	c1nnnn1C=O
Amino_Naphtalimide	c1(N)ccc(C(=O)NC3(=O))c(c3ccc2)c21
Aminonitrile	NC#N
Anhydride	[#6]C(=O)OC(=O)[#6]
Any_Carbazide	O=*N=[N+]=[N-]
aromatic_azides	cN=N=N
Azanitrone	N=[N+]([O-])C
azoalkanals	[N;R0]=[N;R0]CC=O
Azobenzene	c1ccccc1[N!r]=[N!r]c2ccccc2
Azocyanamide	[N;R0]=[N;R0]C#N
b-Carbonyl_Quaternary_Nitrogen	C(=O)CC[N+,n+]
benzylic_quaternary_nitrogen	cC[N+,NX4]
beta-carbonyl_quaternary_nitrogen	C(=O)C[N+,n+,NX4,nX4]
Beta-Fluoro-ethyl-ON	[C;H2$(CF),H1$(C(F)F)]!@[CH2][N,O]
biotin_analogue	C12C(NC(N1)=O)CSC2
carbazides	C(=O)N=N=N
carbodiimides	N=C=N
CCl3-CHO_releasing	C(Cl)(Cl)(Cl)C([O,S])[NX3]
Chloramidine	[Cl]C([C&R0])=N
Conjugated_Dithioether	SC(=[!r])S
Crown_Ether_12CRO4	O1CCOCCOCCOCC1
Crown_Ether_15CRO5	O1CCOCCOCCOCCOCC1
Crown_Ether_16CRO6	O1CCOCCOCCOCCOCCOCC1
crown_ethers	[O;R1][C;R1][C;R1][O;R1][C;R1][C;R1][O;R1]
cyanamide	N[CH2]C#N
Cyanophosphonate	P(OCC)(OCC)(=O)C#N
Cyanohydrin	N#CC[OH1]
di_and_triphosphates	P(=O)([OH])OP(=O)[OH]
Diacetylene	C#CC#C
Diazoalkane	C=[N+]=[N-]
Diazonium_Salt	[N+]#N
Diene	C!@=[CH1]-C!@=[CH1]-[CX3](=O)
Dinitrobenzene_1	c1c([N+](=O)[O-])c([N+](=O)[O-])ccc1
Dinitrobenzene_2	c1c([N+](=O)[O-])ccc([N+](=O)[O-])c1
Dinitrobenzene_3	c1c([N+](=O)[O-])cc([N+](=O)[O-])cc1
disulfides	[SX2][SX2]
Dithiocarbamate	NC(=S)S
Dithiole-2-thione	S1SC=CC1=S
Dithiole-3-thione	S1C=CSC1=C
Dithiomethylene_acetal	S[C;!$(C=*)]S
Enyne	C=!@CC#C
epoxides,_thioepoxides,_aziridines	C1[O,S,N]C1
ester_of_HOBT	C(=O)Onnn
Flavin	c1cccc(NC(=NC(=[N,S,O])NC(=O)3)C3=N2)c12
Fluorescein	c1cc(O)cc(OC(=CC(=O)C=C3)C3=C2)c12
Fluorinated_Carbon_1	C(C(CF)F)F
Fluorinated_Carbon_2	C(C(F)F)(F)F
four_member_lactones	C1(=O)OCC1
geminal_amines	[NH1;!r][CX4][NH1;!r]
geminal_dinitriles	N#CCC#N
halo-pyridine,_-diazoles_and_-triazoles	[Cl,Br,I]c1[c,n][c,n][c,n][c,n]n1
hydrazothiourea	N=NC(S)N
Imidazolium	c1[n+]([#6])ccn1([#6])
Imine2	[#6,#8,#16]-[CH1]=[NH1]
imines_(not_ring)	[#6][C;R0](=[N;R0,O0])[#6]
isocyanates_&_isothiocyanates	N=C=[S,O]
isonitrile	[N+]#[C-]
ketene	C=C=O
Lawesson_Reagent_Derivatives	P(=S)(S)S
methylidene-1,3-dithiole	S1C=CSC1=S
Michael_Phenyl_Ketone	c1ccccc1C(=O)C=!@CC(=O)!@*
N-halo	[NX3,NX4][F,Cl,Br,I]
Nitrobenz-azadiazole_1	c1ccc(n[o,s]n2)c2c1[N+](=O)[O-]
Nitrobenz-azadiazole_2	c1c([N+](=O)[O-])cc(n[o,s]n2)c2c1
nitrosamine	N-[N;X2](=O)
nitroso	[N&D2](=O)
noname	N1=C[S,NH1]C(=[C,N,P][C,N,O,P])C1(=O)
N-Oxide_aliphatic	[N+!$(N=O)][O-X1]
N-S_(not_sulfonamides)	[#6][S;O0][N;H0]
Orthoester	C(O)(O)[OH]
o-tertbutylphenol	c1c([OH1])c(C(C)(C)C)ccc1
Oxobenzothiepine	C1(=O)C=CCSC=C1
P_or_S_Halides	[P,S][Cl,Br,F,I]
p-Aminoaryl_diazo	Nc1aaa(N!@=N)aa1
PCP	PCP
paranitrophenyl_esters	C(=O)Oc1ccc(N(=O)=O)cc1
pentahalophenyl	c1c([F,Cl])c([F,Cl])c([F,Cl])c([F,Cl])c1([F,Cl])
pentafluorophenyl_esters	C(=O)Oc1c(F)c(F)c(F)c(F)c1(F)
peroxide	[#8]~[#8]
Phenanthrene	c12cccc3c1c4c(cc3)cccc4cc2
phosphonate_esters	[#6]P(=O)(~O)O[#6]
phosphoramides	NP(=O)(N)N
phosphorane	C=P
Phosphorus_Halide	[S,P][F,Cl,Br,I]
Polyene	C=!@CC=!@C
polyenes	C=CC=CC=CC=C
polyene_chain_between_aromatics	cC=CC=CC=Cc
polyines	CC#CC#CC
Polynuclear_Aromatic_1	c1cccc(cc(cccc2)c2c3)c13
Polynuclear_Aromatic_2	c1cccc(c(cccc2)c2cc3)c13
Polysulfide	*[SX2][SX2][SX2]*
Sulphur_Halide	[#16][F,Cl,Br,I]
pyrene_fragments	c1c2cccc3c2c4c(cc3)cccc4c1
Pyrylium	c1ccc[o+]c1
reactive_carbonyls	[C;!r](=[O,S])[S;!r]
reactive_carbonyls	[C;!r](=[O,S])[CX2;!r][F,Br,Cl]
Ring_Triple_Bond	[C,c;R]#[C,c;R]
S=N_(not_ring)	[S;R0]=[N;R0]
Sulfonate_Ester	O=[SX4](=O)OC
sulfonyl_cyanide	S(=O)(=O)C#N
Sulphate_Ester	COS(=O)O[C,c]
sulphonates	COS(=O)(=O)[C,c]
Sulphur_Nitrogen_single_bond	[SX2H0]!@[N]
Tetraazinane	C1NNC=NN1
Thiocyanate	SC#N
thioesters	C[O,S;R0][C;R0](=S)
thioles_(not_aromatic)	[!a][SX2;H1]
Thiophosphothionate	P(=S)(-[S;H1,H0$(S(P)C)])(-[O;H1,H0$(O(P)C)])(-N(C)C)
thiourea	[N;!r][C;!r](=S)[N;!r]
Three_Membered_Heterocycle	*1[O,S]*1
Tri_Pentavalent_S	[#16v3,#16v5]
Triacyloxime	C(=O)N(C(=O))OC(=O)
Triazole	c1cnnn1!@C!@[NH1][#6]
triflate	OS(=O)(=O)(C(F)(F)(F))
Triphenyl_Boranyl	B(c1ccccc1)(c2ccccc2)c3ccccc3
triphenylphosphines	P(c1aaaaa1)(c1aaaaa1)(c1aaaaa1)
Triphenyl_Silyl	[Si](c1ccccc1)(c2ccccc2)(c3ccccc3)
Vinyl_Halide	[Cl,Br,I]C=[!O!R]
Vinyl_Sulphone	[#6][CH1]!@=[CH1][S;H1,H0$(S(C)C)](=O)(=O)
sulphates	[#6]S(=O)(=O)O
tropone	C1C(=O)C=CC=CC=1
Oxime	[#6]C(=!@N[$(OC),$([OH])])[#6]
hydrazone	[#6]C(=!@NNa)[#6]
Nitrosone_not_nitro	[$(N(~!@[#6])!@O);!$([N+]([O-])=O)]
Thiocarbonyl_group	C=S
acid_anhydrides_2	[#6]C(=O)!@OC(=!@[N,O])[#6]
trifluroacetate_amide	FC(F)(F)C(=O)N
triple_bond	[#6]C#[CH]
Allene	C=C=C
thiatetrazolidine	[$(Sc1nnn[nH,n-]1),$(Sc1nn[nH,n-]n1)]
oxy-amide	[#6]C(=O)!@C!@C(=O)N
formate_formide	O=[CH][O,N][#6]
pyranone	O=C1C=COC=C1
Coumarin	c1cc2C=CC(=O)Oc2cc1
aminothiazole	s1ccnc1[N!H0]
Thiazolidinone	O=C1CSCN1
Thiomorpholinedione	N1C(=O)CSCC1=O
oxepine	O1C=CC=CC=C1
cyclobutene	C1CC=C1
poly_sub_atomatic	*!@c1c(!@*)c(!@*)c(!@*)c(!@*)c1
Isotopes	[2H,3H,11C,11c,14C,14c,125I,32P,33P,35S]
Undesirable_Elements_Salts	[Ac,Ag,Am,Ar,As,At,Au,Ba,Be,Bi,Bk,Cd,Ce,Cf,Cm,Cr,Cs,Dy,Er, Eu,Fr,Ga,Gd,Ge,He,Hf,Ho,In,Ir,Kr,La,Lu,Mo,Nb,Nd,Ne,Ni, Np,Os,Pa,Pb,Pd,Pm,Po,Pr,Pt,Pu,Ra,Rb,Re,Rh,Rn,Ru,Sb,Sc, Se,Sm,Sr,Ta,Tb,Tc,Te,Th,Ti,Tl,Tm,U,V,W,Xe,Y,Yb,Zr]
Metal_Carbon_bond	[#6;$([#6]~[#3,#11,#12,#13,#19,#20,#26,#27,#28,#29,#30])]
Aromatic_N-Oxide_more_than_one	[n+][O-X1].[n+][O-X1]
Nitro_more_than_one	[N+](=O)[O-].[N+](=O)[O-]
Cyano_gte_2	[C]-[CH0]#[NH0].[C]-[CH0]#[NH0].[C]-[CH0]#[NH0]
Chlor_or_Fluor_gte_5	[Br,Cl,F].[Br,Cl,F].[Br,Cl,F].[Br,Cl,F].[Br,Cl,F].[Br,Cl,F]
Phosphorus_More_Than_1	P.P
gte_2_N_quats	[N,n;H0;+;!$(N~O);!$(n~O)].[N,n;H0;+;!$(N~O);!$(n~O)].[N,n;H0;+;!$(N~O);!$(n~O)]
gte_2_sulfonic_acid	[C,c]S(=O)(=O)[O;D1].[C,c]S(=O)(=O)[O;D1].[C,c]S(=O)(=O)[O;D1]

Details presented within this documentation reproduced from:

ToxAlerts: A Web Server of Structural Alerts for Toxic Chemicals and Compounds with Potential Adverse Reactions Iurii Sushko, Elena Salmina, Vladimir A. Potemkin, Gennadiy Poda, and Igor V. Tetko Journal of Chemical Information and Modeling 2012 52 (8), 2310-2316