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)
CHEMBL1196419			H-AL[Res_2591]-OH name=CHEMBL1196419
CHEMBL2371609			H-MC(1)H{d}FG{d}AR{d}MD{d}R[Leu(4S-5-Me)]{d}S{d}C(1)YR-[NH2] name=CHEMBL2371609
CHEMBL1097668			[NTerm_154]-[MeVal][MeVal][MeVal][Res_1700]{d}[Res_733]-[NH2] name=CHEMBL1097668
CHEMBL2177392			[acetyl]-TGT[Res_1847]GG-OH name=CHEMBL2177392
CHEMBL265891			H-RKKYKMRRK-[NH2] name=CHEMBL265891
CHEMBL1275651			H-GRFKRFRKKFKKLFK-OH name=CHEMBL1275651
CHEMBL3038119			H-{d}[Res_403]L{d}[Res_895][Res_2465]{d}[Res_403]{d}[Res_895][Res_2465]F{d}[Res_895][Res_2465]{d}[Res_403]{d}[Res_895][Res_2465]F{d}[Res_895][Res_2465]{d}[Res_403]{d}[Res_895][Res_2465]{d}[Res_403]{d}[Res_403]{d}[Res_403]{d}[Res_403]-[NH2] name=CHEMBL3038119
CHEMBL607320			H-Y[Res_383]GFL-OH name=CHEMBL607320
CHEMBL1790590			(cyclo)-{d}[Res_78][Res_871][Res_2141]I-(cyclo) name=CHEMBL1790590
CHEMBL438612			[NTerm_820]-I[Res_2314]A-[CTerm_802] name=CHEMBL438612
CHEMBL309188			[NTerm_1419]-V{d}[Res_895][Res_1502]-OH name=CHEMBL309188
CHEMBL370649			[acetyl]-[PhTyr]L{d}PQT-[NH2] name=CHEMBL370649
CHEMBL3086852			H-HA[Res_2480]GTFTSDVSSYLEGQAAKEFIAWLVKGR-[NH2] name=CHEMBL3086852
CHEMBL1187922			H-Y[N(Me)Met]G[Res_1593]P-[NH2] name=CHEMBL1187922
CHEMBL411592			H-V{d}LK-[CTerm_192] name=CHEMBL411592
CHEMBL449545			[acetyl]-KWWPGIFD-[NH2] name=CHEMBL449545
CHEMBL331024			H-{d}C(1){d}FS{d}DT{d}L{d}C(1)-[NH2] name=CHEMBL331024
CHEMBL296603			H-YAFEVVG-OH name=CHEMBL296603
CHEMBL260510			H-IAVPGEVA-OH name=CHEMBL260510
CHEMBL2370351			H-[PyGlu]PLPDCCRQKT-OH name=CHEMBL2370351

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.