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)
CHEMBL1089628			(cyclo)-QRRR[Res_98]{d}[Res_78][Res_1340]RR-(cyclo) name=CHEMBL1089628
CHEMBL525616			H-RWRRKWWWW-OH name=CHEMBL525616
CHEMBL2371120			[NTerm_438]-GGD-OH name=CHEMBL2371120
CHEMBL466147			H-YPAA-[NH2] name=CHEMBL466147
CHEMBL603948			H-RQWIWWWQWWW-[NH2] name=CHEMBL603948
CHEMBL3134581			(cyclo)-{d}[Res_2054]LLVL-(cyclo) name=CHEMBL3134581
CHEMBL499157			H-FGGTGARKSARKLARK-OH name=CHEMBL499157
CHEMBL1197935			(cyclo)-[Res_768][Res_768][Res_768][Res_768][Res_768][Res_768]-(cyclo) name=CHEMBL1197935
CHEMBL1202123			H-[Res_422]PR-[CTerm_364] name=CHEMBL1202123
CHEMBL1183026			H-Y{d}RG-[CTerm_395] name=CHEMBL1183026
CHEMBL438411			H-YPAKPEAPGEDASPEELSRYYASLRHYLNLLTRPRY-OH name=CHEMBL438411
CHEMBL2371005			(cyclo)-[Res_78][Res_2692][Trp(OMe)]I-(cyclo) name=CHEMBL2371005
CHEMBL263315			[NTerm_1262]-WSY{d}WLR{d}P-[CTerm_258] name=CHEMBL263315
CHEMBL43967			[NTerm_433]-GF[MeGly]G-OH name=CHEMBL43967
CHEMBL575372			(cyclo)-F{d}[MeLeu]L{d}VL-(cyclo) name=CHEMBL575372
CHEMBL2371112			[NTerm_438]-GG[Res_1593]-OH name=CHEMBL2371112
CHEMBL355384			[NTerm_585]-L[Res_1534]{d}N-OH name=CHEMBL355384
CHEMBL158470			[NTerm_469]-V[Res_149]V-[CTerm_707] name=CHEMBL158470
CHEMBL573318			[acetyl]-[Res_386]G[MeLeu]M[MeVal]G-[NH2] name=CHEMBL573318
CHEMBL488355			[acetyl]-H{d}[Res_1453]RW-[NH2] name=CHEMBL488355

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.