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)
CHEMBL1075648			[NTerm_1688]-SFQ-[CTerm_789] name=CHEMBL1075648
CHEMBL1170227			H-FKPL[Res_2201]R-OH name=CHEMBL1170227
CHEMBL505820			H-ATRKGYSKF-OH name=CHEMBL505820
CHEMBL151970			[NTerm_820]-L{d}W{d}L-[Unknown_terminal_1] name=CHEMBL151970 inline-mod=C-terminal,[Unknown_terminal_1],H1,QkNGTRECAf9UFQD0/mwAfwoXAPT+bAEAARhSAgABGg==
CHEMBL1288496			(cyclo)-[Res_2558]SIPPICFPDGRCT-(cyclo) name=CHEMBL1288496
CHEMBL268173			[acetyl]-{d}[Res_1340][Res_1788][Res_1343]S{d}[Res_44]{d}[Res_324]L[Res_2151]{d}PA-[NH2] name=CHEMBL268173
CHEMBL2374153			H-NQ{d}[Res_1789]AVGHL{d}M-[NH2] name=CHEMBL2374153
CHEMBL1206620			[NTerm_585]-{d}L{d}[Res_419]{d}[Res_270][MeGly]-OH name=CHEMBL1206620
CHEMBL1625425			H-[Res_1700][Res_2526]P-[CTerm_663] name=CHEMBL1625425
CHEMBL110685			[NTerm_820]-VPV-[CTerm_865] name=CHEMBL110685
CHEMBL395724			H-LVAYPWT-OH name=CHEMBL395724
CHEMBL2370602			H-Y{d}TGFL[Res_1418]-OH name=CHEMBL2370602
CHEMBL2370051			[NTerm_820]-RA{d}WF{d}PP[Nle]-[NH2] name=CHEMBL2370051
CHEMBL283213			H-YSSDTTPA-OH name=CHEMBL283213
CHEMBL2304282			(cyclo)-[MeVal][Res_1246][Abu][MeGly][MeVal]V[MeLeu]A{d}A[MeLeu][MeLeu]-(cyclo) name=CHEMBL2304282
CHEMBL1673384			[acetyl]-KWKSFLKTFKSA{d}VKTVLHTALKAISS-[NH2] name=CHEMBL1673384
CHEMBL2001899			[NTerm_820]-[Res_692][Res_692][Res_692][Res_692][Res_692][Res_1454][Res_692][Res_692][Res_692][Res_692][Res_692]-[CTerm_373] name=CHEMBL2001899
CHEMBL1076232			[NTerm_1335]-W[Nle]DF-[NH2] name=CHEMBL1076232
CHEMBL611125			[NTerm_318]-{d}R{d}R{d}R{d}R{d}R{d}R-OH name=CHEMBL611125
CHEMBL501907			[NTerm_754]-EEE-OH name=CHEMBL501907

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.