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)
CHEMBL1173027H-FFPLAR-OH name=CHEMBL1173027
CHEMBL59028[NTerm_847]-RIAR-[CTerm_1137] name=CHEMBL59028
CHEMBL412401H-R{d}P{d}K{d}PQQ{d}F{d}FG{d}LM-[NH2] name=CHEMBL412401
CHEMBL228754(cyclo)-LLL{d}LF-(cyclo) name=CHEMBL228754
CHEMBL429530H-SVSEIQLMHNLGKHLNSMERV[Res_1500]WLRK(cyclo1)LLQD(cyclo1)V-[NH2] name=CHEMBL429530
CHEMBL2372965[NTerm_887]-VPV-[CTerm_707] name=CHEMBL2372965
CHEMBL2370440[acetyl]-F{d}M[Res_594]{d}[Res_2392][Trp(6-Me)]E[Res_1794]L-[NH2] name=CHEMBL2370440
CHEMBL401163[acetyl]-IC(1)V[Trp(5-OH)]QD[Trp(5-OH)]GAHRC(1)T-[NH2] name=CHEMBL401163
CHEMBL40902[NTerm_700]-FHL-[CTerm_557] name=CHEMBL40902
CHEMBL265013[acetyl]-YAATVINDL-OH name=CHEMBL265013
CHEMBL1221776H-GGS-OH name=CHEMBL1221776
CHEMBL415778H-GKPRPYVPRPTSHPRPIRV-[Unknown_terminal_1] name=CHEMBL415778 inline-mod=C-terminal,[Unknown_terminal_1],H1,QkNGTRECAXAxOAARAGoA8OY5ABEAagEAARhSAgABGg==
CHEMBL514849H-AVAEIQLMHQ[Res_141]AKW-[NH2] name=CHEMBL514849
CHEMBL414283[acetyl]-IC(1)VTQ{d}DWGH{d}HRC(1)T-[NH2] name=CHEMBL414283

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.