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)
CHEMBL3104244			H-G{d}C(1)C(2)SYPPC(1)FATNPDC(2)-[NH2] name=CHEMBL3104244
CHEMBL1254538			[acetyl]-A[Res_601]A-OH name=CHEMBL1254538
CHEMBL446184			H-CV{d}[Res_2470]M-OH name=CHEMBL446184
CHEMBL119992			H-AW[N(Me)Nle]DF-[NH2] name=CHEMBL119992
CHEMBL453406			(cyclo)-NP{d}[Res_1504]LYPI-(cyclo) name=CHEMBL453406
CHEMBL3132973			H-ACYFVCLFEGNDEETCKEWC-OH name=CHEMBL3132973
CHEMBL2371889			H-FV{d}[Res_78]TDVGPFAF-OH name=CHEMBL2371889
CHEMBL183992			H-VPFY-OH name=CHEMBL183992
CHEMBL224109			[NTerm_1061]-GPP-[CTerm_452] name=CHEMBL224109
CHEMBL2372463			(cyclo)-[N(Me)Bmt(E)][Abu][MeGly]V{d}V{d}[MeLeu]A{d}A[MeLeu][MeLeu][MeVal]-(cyclo) name=CHEMBL2372463
CHEMBL2371092			[NTerm_438]-GGGF-OH name=CHEMBL2371092
CHEMBL1957466			(cyclo)-IFGPVT-(cyclo) name=CHEMBL1957466
CHEMBL533798			[acetyl]-A[Res_594]V[Res_594]I[Res_594][Res_594]A[Res_594]-[CTerm_732] name=CHEMBL533798
CHEMBL17948			H-[Res_1700]DSDGK-OH name=CHEMBL17948
CHEMBL78230			[NTerm_481]-[Res_834]{d}[Res_708][Res_140]-OH name=CHEMBL78230
CHEMBL385761			[acetyl]-{d}FHWAVGH-[CTerm_151] name=CHEMBL385761
CHEMBL66664			[acetyl]-[Res_2201]RMMA-[CTerm_1106] name=CHEMBL66664
CHEMBL437920			H-GLGARLQRLLQASGNHAAGILTM-OH name=CHEMBL437920
CHEMBL2104387			H-[Res_1180]V[MeVal]PP-[CTerm_1086] name=CHEMBL2104387
CHEMBL386091			[acetyl]-[Res_820]PKK-[CTerm_1155] name=CHEMBL386091

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.