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)
CHEMBL446259[NTerm_820]-[Res_23][Res_2747]K-[CTerm_586] name=CHEMBL446259
CHEMBL3108895H-AK(cyclo1)TMQTARKSTE(cyclo1)GKAPRKQLA-[NH2] name=CHEMBL3108895
CHEMBL305657[NTerm_579]-[Res_1413][Res_2863]G-[CTerm_810] name=CHEMBL305657
CHEMBL251968(cyclo)-FVV{d}VV-(cyclo) name=CHEMBL251968
CHEMBL2372994H-RR{d}[Res_2506]{d}C(1){d}YR{d}K{d}[Res_2510]{d}PYR{d}[Res_2510]{d}C(1)R-OH name=CHEMBL2372994
CHEMBL412997[NTerm_105]-YGGFLRRIRPK-[NH2] name=CHEMBL412997
CHEMBL388364(cyclo)-FL[Res_1743]{d}VL-(cyclo) name=CHEMBL388364
CHEMBL406290H-[MeGly]R[Res_3014](1)Y{d}[Res_3025](1)HPF-OH name=CHEMBL406290
CHEMBL1631236[acetyl]-EWKRWVQRWKDWLRNLV-[NH2] name=CHEMBL1631236
CHEMBL2372452[NTerm_134]-FAG-[NH2] name=CHEMBL2372452
CHEMBL451917[acetyl]-[Res_1343]{d}[Res_733]{d}[Res_733]{d}[Res_733]-[NH2] name=CHEMBL451917
CHEMBL539209[NTerm_820]-VL[Res_2861]-[CTerm_1150] name=CHEMBL539209
CHEMBL1632439[acetyl]-PVLDEFREK[Res_2789]NEELEALKQKLK-[NH2] name=CHEMBL1632439
CHEMBL501511(cyclo)-PV[Orn]L{d}[Res_765]PV[Orn]L{d}[Res_765]-(cyclo) name=CHEMBL501511
CHEMBL2088510H-[PyGlu]HW[Res_114]HDW[Res_2009]PG-[NH2] name=CHEMBL2088510
CHEMBL2382013(cyclo)-FRFRFRFR-(cyclo) name=CHEMBL2382013
CHEMBL57247[NTerm_1395]-VLS-OH name=CHEMBL57247
CHEMBL3093499[NTerm_157]-[Res_1418]AS[Res_1036]QSL-[CTerm_842] name=CHEMBL3093499

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.