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)
CHEMBL405847			H-PVPVDENDEG-OH name=CHEMBL405847
CHEMBL287423			[NTerm_1362]-F[Res_2867][Res_2201]-[CTerm_170] name=CHEMBL287423
CHEMBL405796			[NTerm_579]-EAVYFAHGDIIW-OH name=CHEMBL405796
CHEMBL40911			[NTerm_1620]-LDT-[NH2] name=CHEMBL40911
CHEMBL1075668			[NTerm_1196]-F[Res_2702]L-[CTerm_810] name=CHEMBL1075668
CHEMBL2369798			[NTerm_601]-SY{d}WLRP-[CTerm_258] name=CHEMBL2369798
CHEMBL2370866			H-GKPRPYSPRP[Res_2220]SHPRPIRV-OH name=CHEMBL2370866
CHEMBL264911			H-KLAQKVKRVLR-OH name=CHEMBL264911
CHEMBL2371831			H-[PyGlu][Res_302]P-[NH2] name=CHEMBL2371831
CHEMBL442094			[NTerm_1671]-R{d}PD-[CTerm_1086] name=CHEMBL442094
CHEMBL1621001			H-[Res_1700]VP-[CTerm_484] name=CHEMBL1621001
CHEMBL2370945			H-TK[Res_2946][Res_1990]-OH name=CHEMBL2370945
CHEMBL252308			H-IC(1)V[Res_1340]QDWGAHRC(1)T-OH name=CHEMBL252308
CHEMBL120264			[NTerm_1688]-[MeVal][Res_1354][Asp(pyrrol-1-yl)][Res_791]-[CTerm_157] name=CHEMBL120264
CHEMBL2147239			[NTerm_1004]-YFEW-[CTerm_1155] name=CHEMBL2147239
CHEMBL1170046			H-FWPLAR-OH name=CHEMBL1170046
CHEMBL1923352			H-KKKSPGEYANIEFG-OH name=CHEMBL1923352
CHEMBL339157			H-[Res_1700]FLLR-[NH2] name=CHEMBL339157
CHEMBL340930			H-{d}W{d}QMG{d}H{d}S-OH name=CHEMBL340930
CHEMBL2369384			[acetyl]-HWAVGH-[CTerm_234] name=CHEMBL2369384

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.