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)
CHEMBL1254458[acetyl]-A[Res_2133]A-[CTerm_1155] name=CHEMBL1254458
CHEMBL286519[NTerm_718]-V{d}[Res_78]D-[CTerm_563] name=CHEMBL286519
CHEMBL1917689H-[Trp_mod][Nle]EAAYQRFL-OH name=CHEMBL1917689
CHEMBL2370067H-{d}[Res_1724]LDIIW-[Unknown_terminal_1] name=CHEMBL2370067 inline-mod=C-terminal,[Unknown_terminal_1],H1,QkNGTRECAc/vAQBQ/10AT6UDAFD/XQEAARhSAgABGg==
CHEMBL408280[acetyl]-{d}[Res_1340]F{d}FSYRFR{d}PA-[NH2] name=CHEMBL408280
CHEMBL2403631[NTerm_836]-[Res_1354][Res_1560][Res_1514]-[CTerm_1100] name=CHEMBL2403631
CHEMBL335383[NTerm_136]-[Res_1354][Asp(pyrrol-1-yl)]D-[CTerm_1243] name=CHEMBL335383
CHEMBL1450785H-[Res_1700]VS-[CTerm_390] name=CHEMBL1450785
CHEMBL2372871[NTerm_1693]-GGPEG-OH name=CHEMBL2372871
CHEMBL324347H-{d}YIGSR-[NH2] name=CHEMBL324347
CHEMBL207669[NTerm_820]-I[Res_122]A-[CTerm_802] name=CHEMBL207669
CHEMBL257527[NTerm_262]-RRID-[CTerm_386] name=CHEMBL257527
CHEMBL170229[NTerm_585]-L[Res_1534]L-OH name=CHEMBL170229
CHEMBL2011463(cyclo)-Y{d}WKV{d}[Res_733][Res_1700]-(cyclo) name=CHEMBL2011463
CHEMBL1808933[NTerm_1463]-RVK-[CTerm_806] name=CHEMBL1808933

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.