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)
CHEMBL2370901H-[MeGly]RVY{d}[Res_2077]HPI-OH name=CHEMBL2370901
CHEMBL484920[NTerm_195]-LFL-[CTerm_855] name=CHEMBL484920
CHEMBL415587H-RPKP{d}QQF{d}FG{d}LM-[NH2] name=CHEMBL415587
CHEMBL2304033H-D{d}SDP{d}R-OH name=CHEMBL2304033
CHEMBL292761H-R{d}Y{d}L{d}P{d}[Res_872]-OH name=CHEMBL292761
CHEMBL437988[acetyl]-F[Orn]P{d}[Res_1667]{d}[Res_870]{d}F-[NH2] name=CHEMBL437988
CHEMBL2035775H-LLGGPS-OH name=CHEMBL2035775
CHEMBL2371784(cyclo)-[Res_1450][Res_2478][MeGly][MeLeu]V[MeLeu]A{d}A[MeLeu][MeLeu][MeVal]-(cyclo) name=CHEMBL2371784
CHEMBL2147227[acetyl]-EYFEW-[CTerm_1155] name=CHEMBL2147227
CHEMBL442094[NTerm_1671]-R{d}PD-[CTerm_1086] name=CHEMBL442094
CHEMBL2370301H-{d}F{d}C(1){d}YW{d}KVC(1)T-[NH2] name=CHEMBL2370301
CHEMBL410965H-{d}YGDY[Nle][Res_2269]W[Nle]D[Res_2269]-OH name=CHEMBL410965
CHEMBL1624649H-[Res_1700]{d}VP-[CTerm_980] name=CHEMBL1624649
CHEMBL117436H-{d}C(1){d}RT{d}DT{d}L{d}C(1)-[NH2] name=CHEMBL117436
CHEMBL2304098H-RPKPQQ{d}WW{d}WL{d}M-OH name=CHEMBL2304098

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.