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 ID	ChEMBL structure	Converted sequence image	Proteax PLN (Protein Line Notation)
CHEMBL1977629			[NTerm_700]-FFL-[CTerm_663] name=CHEMBL1977629
CHEMBL2371212			H-F{d}C(1){d}[Res_202]{d}W{d}KT[Res_3018](1)T-[NH2] name=CHEMBL2371212
CHEMBL411230			H-RPK{d}PQQF{d}[Res_23]GLM-[NH2] name=CHEMBL411230
CHEMBL375109			H-LYENKPRRPYIL-OH name=CHEMBL375109
CHEMBL407766			H-SS{d}C(1){d}A{d}FGG{d}RIGRI{d}C(1){d}F{d}R-OH name=CHEMBL407766
CHEMBL568900			H-MNWNI-OH name=CHEMBL568900
CHEMBL228754			(cyclo)-LLL{d}LF-(cyclo) name=CHEMBL228754
CHEMBL3098667			[NTerm_148]-RLIF-OH name=CHEMBL3098667
CHEMBL2372318			H-FLP-[CTerm_810] name=CHEMBL2372318
CHEMBL304082			H-Y[Res_434]GFM-[NH2] name=CHEMBL304082
CHEMBL446844			H-SPMFKGV-[CTerm_423] name=CHEMBL446844
CHEMBL434111			H-Y[Res_1579]F[MeGly]-[CTerm_616] name=CHEMBL434111
CHEMBL2373979			H-SSC(1){d}FGGRID{d}RIGA{d}QSGLC(1)[Cys(Me)]NSFR-[NH2] name=CHEMBL2373979
CHEMBL1791264			H-[MeGly]RVYIH[Res_78]I-OH name=CHEMBL1791264
CHEMBL433919			[NTerm_436]-[Res_1053]N-[CTerm_827] name=CHEMBL433919
CHEMBL437465			H-HSQGTFC(1)SDYSC(1)YLDSRRAQDFVQWLMNT-OH name=CHEMBL437465
CHEMBL304228			H-GRGDF-OH name=CHEMBL304228
CHEMBL131814			H-YGGFMG-[NH2] name=CHEMBL131814
CHEMBL1185666			[NTerm_1066]-LAL-[CTerm_842] name=CHEMBL1185666
CHEMBL506117			H-FVWQKGTNR-OH name=CHEMBL506117

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:

N-terminals, 1699 structures, 420 kB
C-terminals, 1270 structures, 333 kB
Residues, 3030 structures, 726 kB

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:

Residue names update script, 143 name assigments, 18 kB

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.