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)
CHEMBL509042H-[Res_1340][Res_3018](1)F{d}W[Orn]YC(1)V-OH name=CHEMBL509042
CHEMBL216363(cyclo)-[N(Me)Bmt(E)][Abu][MeGly][MeLeu]V[MeLeu]A[Res_356][MeLeu][MeLeu][MeVal]-(cyclo) name=CHEMBL216363
CHEMBL414319H-[Res_1496]LIGRLI-[NH2] name=CHEMBL414319
CHEMBL2381404[acetyl]-MPRFMDYWEGLN-[NH2] name=CHEMBL2381404
CHEMBL2371104[NTerm_438]-GGG[Res_2600]-OH name=CHEMBL2371104
CHEMBL1183449H-RYLP-[CTerm_1035] name=CHEMBL1183449
CHEMBL2373085[acetyl]-[Res_1601]PDIIW-OH name=CHEMBL2373085
CHEMBL1556461H-A[Res_2708]R[Res_2201][Res_141]Y-[NH2] name=CHEMBL1556461
CHEMBL3104638H-AC(1)F{d}[Res_625]KYC(1)V-OH name=CHEMBL3104638
CHEMBL287753[acetyl]-W[Res_1226]DF-[NH2] name=CHEMBL287753
CHEMBL325232[NTerm_700]-ELC-[CTerm_1086] name=CHEMBL325232
CHEMBL2418221H-GRGDTP-OH name=CHEMBL2418221
CHEMBL68566[acetyl]-[Res_2201]RA-[NH2] name=CHEMBL68566
CHEMBL293946[NTerm_820]-LET-[CTerm_1095] name=CHEMBL293946

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.