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.



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20 randomly selected converted structures

ChEMBL IDChEMBL structureConverted sequence imageProteax PLN (Protein Line Notation)
CHEMBL2371280H-C(1)YIQNC(1)PLG-[CTerm_450] name=CHEMBL2371280
CHEMBL427923H-[PyGlu]GPPISIDLPLILLRKMIEIEKQEKEKQQAANNRLLLDTI-OH name=CHEMBL427923
CHEMBL583935H-{d}C(1){d}DG[Tyr(3,5-diBr)]G[Res_1418]N{d}C(1)-[NH2] name=CHEMBL583935
CHEMBL1923393H-DYFEW-OH name=CHEMBL1923393
CHEMBL376361[NTerm_1634]-PGG-OH name=CHEMBL376361
CHEMBL441199H-GPGGPA-[CTerm_723] name=CHEMBL441199
CHEMBL2205674H-RWRWRWK-[NH2] name=CHEMBL2205674
CHEMBL378323(cyclo)-AFPGLHF-(cyclo) name=CHEMBL378323
CHEMBL2371523[acetyl]-[Res_3012](1)N{d}PRGD[Res_2141]RC(1)-[NH2] name=CHEMBL2371523
CHEMBL2370108H-RR[Res_1340]C(1)Y{d}[Res_2510]K{d}KPYR{d}[Res_2510]C(1)R-OH name=CHEMBL2370108
CHEMBL506211(cyclo)-{d}P{d}[Res_2141]{d}WF-(cyclo) name=CHEMBL506211
CHEMBL1645422H-SSRLESW[Res_1788]AGEKESRG-OH name=CHEMBL1645422
CHEMBL262829H-TAYFLLKLAGRA-OH name=CHEMBL262829
CHEMBL2373018[NTerm_774]-V{d}[Res_78]DP-[CTerm_165] name=CHEMBL2373018
CHEMBL2371119[NTerm_438]-GGE-OH name=CHEMBL2371119
CHEMBL429011[NTerm_1209]-AL{d}C(1){d}DN{d}PRID{d}RW{d}Y{d}C(1)QFVEG-[NH2] name=CHEMBL429011
CHEMBL2372747[NTerm_808]-KIA[Abu]-OH name=CHEMBL2372747
CHEMBL525212H-{d}[Res_3018](1)SIYDPGDDI{d}KC(1)-OH name=CHEMBL525212
CHEMBL323857H-YIG-[CTerm_72] name=CHEMBL323857
CHEMBL100799[NTerm_283]-F[Res_360]P-OH name=CHEMBL100799

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.