Converting ChEMBL to sequence

This page gives you access to a subset of ChEMBL that has been converted to Protein Line Notation. A total of 27142 structures out of 39123 "peptide-like" structures have been successfully converted. More details on the conversion process can be found beneath the structure table.


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20 randomly selected converted structures

ChEMBL IDChEMBL structureConverted sequence imageProteax PLN (Protein Line Notation)
CHEMBL411648(cyclo)-[N(Me)Bmt(E)][Abu][MeGly][MeLeu]V[MeLeu]A[Res_1288][MeLeu][MeLeu][MeVal]-(cyclo) name=CHEMBL411648
CHEMBL420380[NTerm_611]-FVAL-[NH2] name=CHEMBL420380
CHEMBL3125140[NTerm_152]-[Res_1354][Res_1037][Res_1514]-[CTerm_1100] name=CHEMBL3125140
CHEMBL524521H-HSDGIATDSYSRYRKQMAVKKYLAAVL-[NH2] name=CHEMBL524521
CHEMBL410279[NTerm_538]-AL{d}C(1){d}DN{d}PRID{d}RW{d}Y{d}C(1)QFVEG-[NH2] name=CHEMBL410279
CHEMBL473032[NTerm_577]-[Res_2808]AD-[CTerm_1090] name=CHEMBL473032
CHEMBL3040333[NTerm_1586]-VVD-OH name=CHEMBL3040333
CHEMBL301153[NTerm_18]-{d}V{d}A{d}E{d}F-OH name=CHEMBL301153
CHEMBL216259[NTerm_1221]-KKYIKVFVFK-[NH2] name=CHEMBL216259
CHEMBL501575H-[Res_368]RPYIL-OH name=CHEMBL501575
CHEMBL108873[NTerm_1620]-VPV-[CTerm_1134] name=CHEMBL108873
CHEMBL216788H-{d}R{d}PKPQQ{d}F{d}FGLM-[NH2] name=CHEMBL216788
CHEMBL116690[NTerm_700]-{d}V{d}L[Res_2639]-[CTerm_766] name=CHEMBL116690
CHEMBL390321H-FKTFLKWLHRF-[NH2] name=CHEMBL390321
CHEMBL266077[acetyl]-RHYINLITRQRY-OH name=CHEMBL266077
CHEMBL266899H-[MeGly]RVYVH{d}PF-OH name=CHEMBL266899
CHEMBL3115755[NTerm_1303]-{d}V{d}[Res_1286]G{d}S{d}WS[Res_1286]{d}[Res_1286]FEVIA-OH name=CHEMBL3115755
CHEMBL385689H-[Res_1340]C(1)[Res_1343]{d}WK{d}V{d}C(1)[Res_2708]-[NH2] name=CHEMBL385689
CHEMBL2370919H-RPKPQQF[Res_2600]GL[Nle]-[NH2] name=CHEMBL2370919
CHEMBL95363[acetyl]-LL[Res_1828]-[Unknown_terminal_1] name=CHEMBL95363 inline-mod=C-terminal,[Unknown_terminal_1],H1,QkNGTRECAYCQHABYAA4AAEYeAFgADgEAARhSAgABGg==

Conversion process

All structures in the ChEMBL 19 database were downloaded as an SD file and, with the help of KNIME, probable "peptide-like" structures were identified. The "peptide-like" structures were defined as those containing a substructure of three connected glysines. This yielded a "peptide-like" subset of 39123 structures.

The peptide subset was loaded into a PostgreSQL database table and the Biochemfusion Proteax cartridge was used to convert structures, when possible, to sequences. The first conversion took 87 seconds and produced 27142 converted sequences.

You can download the full set of produced sequences (TAB-separated file with ChEMBL ID + PLN, ~11MB).

All found unknown residues and terminal structures were embedded as inline structures in the first round of produced PLN. The embedded structures were then de-duplicated and extracted. You can download the structure sets in gzip-ed SD file format from here:

143 of the unknown residue structures have been assigned well-defined names by NextMove Software's great Sugar & Splice tool (press the "Biologics" button). Many thanks to Roger Sayle at NextMove Software for processing this subset of residues with Sugar & Splice.

NextMove's residue names can be applied to a Proteax modification database (where the above SD files have been imported) by the following SQL script:

The currently produced PLN has been generated after all the above data has been loaded into Proteax's database of known structures. As you will see, most of the non-natural residues and terminals have auto-generated names based on sequential numbers.