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)
CHEMBL2372380			H-{d}P{d}[Res_895]ARNDQEGHILKMFPSTWYV-OH name=CHEMBL2372380
CHEMBL2396874			H-G[Res_760]LKRIKTLL-[NH2] name=CHEMBL2396874
CHEMBL407127			[NTerm_621]-[Res_2592]SKKKK-[NH2] name=CHEMBL407127
CHEMBL2370441			[NTerm_700]-[Res_2240][Nle]GW[Res_2175]DF-[NH2] name=CHEMBL2370441
CHEMBL1345137			[NTerm_820]-{d}APLG-[NH2] name=CHEMBL1345137
CHEMBL264122			[NTerm_1688]-HWAV{d}AH-[CTerm_461] name=CHEMBL264122
CHEMBL525207			H-HS[Res_2987]GIFTDSYSRYRKQMAVKKYLAAVL-[NH2] name=CHEMBL525207
CHEMBL1083904			[NTerm_1564]-[Res_1036][Res_1354][Res_1809]-[CTerm_979] name=CHEMBL1083904
CHEMBL378045			H-TITYDL-OH name=CHEMBL378045
CHEMBL235440			H-SLIGRFI-[NH2] name=CHEMBL235440
CHEMBL2372155			H-RPPGFSP[Res_2201]-OH name=CHEMBL2372155
CHEMBL438512			[NTerm_1395]-LIGRLI-[NH2] name=CHEMBL438512
CHEMBL1607541			H-[Res_1700]VQ-[CTerm_390] name=CHEMBL1607541
CHEMBL511009			H-RWRWWIKII-OH name=CHEMBL511009
CHEMBL584600			(cyclo)-{d}F{d}[Res_488]L{d}V{d}L-(cyclo) name=CHEMBL584600
CHEMBL1082139			[NTerm_1688]-SFS-OH name=CHEMBL1082139
CHEMBL508365			H-TAAERRRKKR-OH name=CHEMBL508365
CHEMBL477183			[NTerm_700]-GGGG-[CTerm_663] name=CHEMBL477183
CHEMBL386271			[acetyl]-[Nle]EHFRWGKPV-[NH2] name=CHEMBL386271
CHEMBL1373744			H-[Res_1700][Abu]P-[CTerm_390] name=CHEMBL1373744

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.