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

Search is done within records with converted sequences only. Result listing is limited to max. 100 records.

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20 randomly selected converted structures

ChEMBL ID	ChEMBL structure	Converted sequence image	Proteax PLN (Protein Line Notation)
CHEMBL1796780			H-GIF[Res_1536]EQ-OH name=CHEMBL1796780
CHEMBL332033			[NTerm_1688]-GV[Asp(pyrrol-1-yl)]DL-OH name=CHEMBL332033
CHEMBL2440171			[NTerm_986]-RK[Nle]-[NH2] name=CHEMBL2440171
CHEMBL2371207			[NTerm_1254]-AAPV-[CTerm_707] name=CHEMBL2371207
CHEMBL1945784			H-C(1)GAKHVPC(1)YFVGIGTPISFE-OH name=CHEMBL1945784
CHEMBL1221893			H-P[Res_1418]P-OH name=CHEMBL1221893
CHEMBL1076026			[NTerm_274]-YGY-[CTerm_1213] name=CHEMBL1076026
CHEMBL447587			H-PMMGKASPV-[CTerm_423] name=CHEMBL447587
CHEMBL265836			H-{d}C(1){d}K{d}FFW[Res_837]TFC(1)-OH name=CHEMBL265836
CHEMBL1790666			[NTerm_387]-PIV-[NH2] name=CHEMBL1790666
CHEMBL1835404			[acetyl]-VDV[Res_2238]-[CTerm_1229] name=CHEMBL1835404
CHEMBL2028967			H-{d}[Res_966]{d}[Res_895][Res_1743]-[CTerm_1086] name=CHEMBL2028967
CHEMBL2221069			(cyclo)-{d}[Res_1276]R[Res_1340]G{d}Y-(cyclo) name=CHEMBL2221069
CHEMBL20579			H-YVV[Asp(pyrrol-1-yl)]DL-OH name=CHEMBL20579
CHEMBL2372894			[NTerm_1693]-EGPEG-OH name=CHEMBL2372894
CHEMBL1909034			H-DFDMLRC(1)MLGRVFRPC(1)W-[CTerm_270] name=CHEMBL1909034
CHEMBL1223109			[NTerm_820]-VAD-[CTerm_1159] name=CHEMBL1223109
CHEMBL1773090			[NTerm_1485]-Y[Res_2243]C(1)-[NH2].[NTerm_1485]-Y[Res_2243]C(1)-[NH2] name=CHEMBL1773090
CHEMBL438576			H-{d}C(1){d}K{d}FF[Res_1340][Res_837]TFTS[N(Me)Cys](1)-OH name=CHEMBL438576
CHEMBL257934			[NTerm_700]-LLY-[CTerm_121] name=CHEMBL257934

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.