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)
CHEMBL1214974[NTerm_799]-C(1)PF-[CTerm_59].[NTerm_799]-C(1)PF-[CTerm_59] name=CHEMBL1214974
CHEMBL368530H-YMG[Res_1593]P-[NH2] name=CHEMBL368530
CHEMBL1271522H-FAK-OH name=CHEMBL1271522
CHEMBL408568H-GC(1)C(2)SNPVC(1)HLEHSNLC(2)-OH name=CHEMBL408568
CHEMBL1990293[acetyl]-[Res_2608][Res_2608][Res_2608][Res_2608][Res_2608][Res_1454][Res_2608][Res_2608][Res_2608][Res_2608][Res_2608]-[NH2] name=CHEMBL1990293
CHEMBL475845(cyclo)-II[Res_1562]F-(cyclo) name=CHEMBL475845
CHEMBL1933627[NTerm_122]-GFGFP-[CTerm_1156] name=CHEMBL1933627
CHEMBL574923[NTerm_820]-SSKAL-[Unknown_terminal_1] name=CHEMBL574923 inline-mod=C-terminal,[Unknown_terminal_1],H1,QkNGTRECAc/hFwDo/88AT5cZAOj/zwEAARhSAgABGg==
CHEMBL2369724(cyclo)-[N(Me)Bmt(E)][Abu][MeGly]{d}[MeLeu]{d}V{d}[MeLeu]A{d}A[MeLeu][MeLeu]{d}[Res_386]-(cyclo) name=CHEMBL2369724
CHEMBL509556H-{d}APGAAAPGA-[NH2] name=CHEMBL509556
CHEMBL373124[acetyl]-[PhTyr]LP-[CTerm_1012] name=CHEMBL373124
CHEMBL341015H-DSFVG-[CTerm_1171] name=CHEMBL341015
CHEMBL405753[NTerm_579]-EAVYFAHLDIGW-OH name=CHEMBL405753
CHEMBL299252[NTerm_1362]-F[Res_467][Res_2201]-[CTerm_170] name=CHEMBL299252
CHEMBL499397H-H[Res_725][Res_725]GTFTSDVSSYLEGQAAKEFIAWLVKGR-[NH2] name=CHEMBL499397
CHEMBL44307[NTerm_433]-GFG[MeGly]-OH name=CHEMBL44307
CHEMBL506645H-QRFSTGHFGGLYPSNGP-OH name=CHEMBL506645
CHEMBL1807685H-FGK-OH name=CHEMBL1807685
CHEMBL511066H-R[Res_1118]R-[CTerm_1086] name=CHEMBL511066
CHEMBL2373044[acetyl]-YLR-[Unknown_terminal_1] name=CHEMBL2373044 inline-mod=C-terminal,[Unknown_terminal_1],H1,QkNGTRECAV/9CQCr/PMA37ILAKv88wEAARhSAgABGg==

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.