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)
CHEMBL438194[acetyl]-{d}[Res_272]LDIIW-OH name=CHEMBL438194
CHEMBL40886H-CV[Res_2636]-[CTerm_810] name=CHEMBL40886
CHEMBL454510[NTerm_410]-SWGC[Tyr(3-NO2)]-[NH2] name=CHEMBL454510
CHEMBL2316219H-[Res_1700][Res_1036][Res_1668]-[CTerm_866] name=CHEMBL2316219
CHEMBL2049150[NTerm_923]-RVR-[CTerm_259] name=CHEMBL2049150
CHEMBL2391753[NTerm_1496]-KAAFA[Abu]AAK-OH name=CHEMBL2391753
CHEMBL1625449H-[Res_1700]VP-[CTerm_536] name=CHEMBL1625449
CHEMBL245123[NTerm_700]-[Res_1354][Res_290]{d}[Res_2639]-OH name=CHEMBL245123
CHEMBL534026(cyclo)-{d}AV[Orn]L{d}FP{d}AV[Orn]L{d}FP-(cyclo) name=CHEMBL534026
CHEMBL500506H-TPQRARRRKKRD-OH name=CHEMBL500506
CHEMBL275323[acetyl]-HWAVGH-[CTerm_560] name=CHEMBL275323
CHEMBL405664[NTerm_469]-VPV-[CTerm_282] name=CHEMBL405664
CHEMBL510129(cyclo)-{d}[Res_1700][Res_737]I[Res_1700][MeLeu]A[Res_1700]-(cyclo) name=CHEMBL510129
CHEMBL474732H-GAPAPG-[NH2] name=CHEMBL474732
CHEMBL1744403[NTerm_958]-I[Res_2360]G-OH name=CHEMBL1744403
CHEMBL6779[NTerm_1518]-MLF-OH name=CHEMBL6779
CHEMBL13665H-{d}[Res_1892]AG{d}F{d}L-OH name=CHEMBL13665
CHEMBL509327H-KRKLIRWWW-OH name=CHEMBL509327
CHEMBL557629H-DFDMLRC(1)MLGRVFRPC(1)W-[CTerm_163] name=CHEMBL557629
CHEMBL2425394H-QKASPGA-OH name=CHEMBL2425394

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.