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.

ChEMBL ID contains
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20 randomly selected converted structures

ChEMBL IDChEMBL structureConverted sequence imageProteax PLN (Protein Line Notation)
CHEMBL438604(cyclo)-F{d}F[Res_1200]{d}FYV[Orn][MeGly]{d}FP-(cyclo) name=CHEMBL438604
CHEMBL414477H-Y{d}DGF{d}[Res_403]RRIRPK-[NH2] name=CHEMBL414477
CHEMBL388364(cyclo)-FL[Res_1743]{d}VL-(cyclo) name=CHEMBL388364
CHEMBL1170645H-FLT{d}[Res_2201]AR-OH name=CHEMBL1170645
CHEMBL1688626[NTerm_484]-ETAV-OH name=CHEMBL1688626
CHEMBL557243H-Y[Res_787]FF-[NH2] name=CHEMBL557243
CHEMBL297242H-{d}K{d}[Res_3029][MeVal][Res_245]M-OH name=CHEMBL297242
CHEMBL3038101H-RRP[Res_1418]G[Res_2944]S{d}F[Res_1285]R-OH name=CHEMBL3038101
CHEMBL2068782[acetyl]-DKWKAVYDKFAEAFKEFL-[NH2] name=CHEMBL2068782
CHEMBL2369816[NTerm_1650]-[Nle]GW[Nle][Res_2987]F-[NH2] name=CHEMBL2369816
CHEMBL2371500H-[Res_3011](1)G{d}HRGD{d}LRC(1)R-OH name=CHEMBL2371500
CHEMBL1793839H-RRPY{d}IF-OH name=CHEMBL1793839
CHEMBL2114215[acetyl]-H{d}LDIIW-OH name=CHEMBL2114215
CHEMBL1818533[formyl]-M[Res_543][Thr(tBu)]G[Res_322]AL-[CTerm_1197] name=CHEMBL1818533
CHEMBL506112H-HYRWGKFV-[NH2] name=CHEMBL506112
CHEMBL3134254[NTerm_820]-AL[Res_1313]-[Unknown_terminal_1] name=CHEMBL3134254 inline-mod=C-terminal,[Unknown_terminal_1],H1,QkNGTRECAe9dNwB6/9wAbxM5AHr/3AEAARhSAgABGg==
CHEMBL263035H-{d}[Res_1788]AY{d}WKVA{d}F-[NH2] name=CHEMBL263035
CHEMBL2372654[NTerm_808]-KPI[Res_2179]-OH name=CHEMBL2372654

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.