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 ID	ChEMBL structure	Converted sequence image	Proteax PLN (Protein Line Notation)
CHEMBL367094			[NTerm_700]-DPF-[CTerm_394] name=CHEMBL367094
CHEMBL427658			H-{d}C(1){d}K{d}FF[Res_1340][Res_2253]TFTSC(1)-OH name=CHEMBL427658
CHEMBL338294			(cyclo)-[Res_733]P{d}FI[Res_78]K-(cyclo) name=CHEMBL338294
CHEMBL227251			H-R[Res_272]R-[CTerm_26] name=CHEMBL227251
CHEMBL240668			(cyclo)-KWWKFK-(cyclo) name=CHEMBL240668
CHEMBL1689478			[acetyl]-FEVC(1)HYIRLPHC(1)TRY-[NH2] name=CHEMBL1689478
CHEMBL2372153			H-RPPGFSP{d}[Res_2141]R-OH name=CHEMBL2372153
CHEMBL412701			H-R{d}PKP{d}Q{d}QF{d}FGLM-[NH2] name=CHEMBL412701
CHEMBL2203699			(cyclo)-F[Res_733]{d}[Res_1805]VL-(cyclo) name=CHEMBL2203699
CHEMBL382409			H-YPGW[N(Me)Nle]DF-[NH2] name=CHEMBL382409
CHEMBL416247			H-CV{d}[Res_583]-[CTerm_810] name=CHEMBL416247
CHEMBL2368927			H-ACSTERRYCPIEIFPCG-[NH2] name=CHEMBL2368927
CHEMBL1802435			H-GGFSFAF-[NH2] name=CHEMBL1802435
CHEMBL294354			[NTerm_700]-W[Res_410]DF-[NH2] name=CHEMBL294354
CHEMBL1830314			H-LRRFSTMPFMFANINNVANF-OH name=CHEMBL1830314
CHEMBL2407372			H-[Res_1095][Res_2801]I-[CTerm_810] name=CHEMBL2407372
CHEMBL3134578			(cyclo)-YLLVL-(cyclo) name=CHEMBL3134578
CHEMBL446555			H-GRIGGKNVR-OH name=CHEMBL446555
CHEMBL1254032			[acetyl]-A[Res_2503]A-OH name=CHEMBL1254032
CHEMBL83692			(cyclo)-[Res_686][Res_1296]-(cyclo) name=CHEMBL83692

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:

N-terminals, 1699 structures, 420 kB
C-terminals, 1270 structures, 333 kB
Residues, 3030 structures, 726 kB

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:

Residue names update script, 143 name assigments, 18 kB

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.