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.

Refresh page with an empty search box to get 100 random structures.

20 randomly selected converted structures

ChEMBL ID	ChEMBL structure	Converted sequence image	Proteax PLN (Protein Line Notation)
CHEMBL337970			H-DSFVG-[CTerm_981] name=CHEMBL337970
CHEMBL1569041			H-[Res_1700]{d}VP-[CTerm_783] name=CHEMBL1569041
CHEMBL100221			[NTerm_1565]-ALYD-[NH2] name=CHEMBL100221
CHEMBL252926			[acetyl]-IC(1)VYQDWGAHRC(1)T-[NH2] name=CHEMBL252926
CHEMBL2373993			[NTerm_345]-[Res_2232]FVNR{d}PRR-[NH2] name=CHEMBL2373993
CHEMBL2440152			[NTerm_440]-RK[Nle]-[NH2] name=CHEMBL2440152
CHEMBL2371058			[NTerm_965]-{d}YC(1){d}F[Res_1543]WKTFC(1)-OH name=CHEMBL2371058
CHEMBL406889			[NTerm_700]-NR{d}FF{d}WLM-[CTerm_810] name=CHEMBL406889
CHEMBL413676			H-YP[Phe(2-Me)]F-[NH2] name=CHEMBL413676
CHEMBL1081570			[NTerm_1688]-AFQ-[CTerm_716] name=CHEMBL1081570
CHEMBL413633			H-FQGVLQAVRFVF-OH name=CHEMBL413633
CHEMBL2372484			(cyclo)-[Res_1537][Abu][MeGly]{d}[Res_733]{d}V{d}[MeLeu]A{d}A[MeLeu][MeLeu][MeVal]-(cyclo) name=CHEMBL2372484
CHEMBL172849			[NTerm_700]-VPF-[CTerm_118] name=CHEMBL172849
CHEMBL2103901			H-KLLLLKLLLLKLLLLKLLLLK-OH name=CHEMBL2103901
CHEMBL406033			H-{d}FFF{d}WKTFT-[NH2] name=CHEMBL406033
CHEMBL410361			H-{d}R{d}PK{d}P{d}QQF{d}FG{d}LM-[NH2] name=CHEMBL410361
CHEMBL389532			[NTerm_700]-V[Res_1037][Res_1514]-[CTerm_1059] name=CHEMBL389532
CHEMBL2205675			H-RWRWRW[Res_2177]-[NH2] name=CHEMBL2205675
CHEMBL3085494			[NTerm_820]-RP[Res_1743]PQQ{d}W{d}WG{d}L{d}M-[CTerm_810] name=CHEMBL3085494
CHEMBL2372600			[NTerm_1140]-FGGRIDRIGAQ{d}SGLG{d}[Res_3018]NSFRY-OH name=CHEMBL2372600

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.