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)
CHEMBL2371075			[NTerm_438]-GGGP-OH name=CHEMBL2371075
CHEMBL288116			[NTerm_291]-[Res_1053]N-[CTerm_15] name=CHEMBL288116
CHEMBL2372975			[NTerm_537]-VPV-[CTerm_707] name=CHEMBL2372975
CHEMBL427748			H-{d}C(1)S{d}C(2)S{d}SL{d}MD{d}KE{d}C(2)V{d}YFC(1)HLDLIW-OH name=CHEMBL427748
CHEMBL527049			H-MAGRSGDSDEELLKTVRLIKFLYQSNPPPS-OH name=CHEMBL527049
CHEMBL2336576			H-AWLAYPGAVSYR-OH name=CHEMBL2336576
CHEMBL1345716			[NTerm_820]-G[Res_1804]P-[CTerm_663] name=CHEMBL1345716
CHEMBL1319073			H-AVV-[CTerm_861] name=CHEMBL1319073
CHEMBL2371521			[acetyl]-{d}C(1){d}NP{d}RG{d}D{d}[Res_2141]E{d}C(1)-[NH2] name=CHEMBL2371521
CHEMBL2372667			H-FC(1)F{d}W{d}W{d}KT{d}F[Res_3020](1)-[NH2] name=CHEMBL2372667
CHEMBL2371345			[acetyl]-{d}[Res_1340]{d}[Res_2708]{d}[Res_1340]SY[Res_312]LRPG-[NH2] name=CHEMBL2371345
CHEMBL289744			[NTerm_700]-W{d}[Res_503][Res_2987]F-[NH2] name=CHEMBL289744
CHEMBL227039			H-RPGLLD-OH name=CHEMBL227039
CHEMBL2371955			H-[Res_977]A{d}M-OH name=CHEMBL2371955
CHEMBL583929			(cyclo)-L{d}V{d}L{d}FL{d}L{d}V{d}LFL-(cyclo) name=CHEMBL583929
CHEMBL1178130			H-Y{d}RG-[CTerm_724] name=CHEMBL1178130
CHEMBL2063863			H-[Res_1700][Res_1036][Res_510]-[CTerm_1] name=CHEMBL2063863
CHEMBL1607295			H-[Res_1700]LP-[CTerm_390] name=CHEMBL1607295
CHEMBL2396708			H-EHWSYGLRPG-[CTerm_786] name=CHEMBL2396708
CHEMBL385031			[acetyl]-[Res_1340][Res_1788][Res_1343]S[Res_1384][Res_2763]LR{d}PA-OH name=CHEMBL385031

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.