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)
CHEMBL219201			[NTerm_965]-{d}FC(1){d}[Res_143]{d}WKTC(1)T-[NH2] name=CHEMBL219201
CHEMBL3041108			H-[PyGlu][Res_2767]P-[NH2] name=CHEMBL3041108
CHEMBL1688612			[NTerm_565]-ETDV-OH name=CHEMBL1688612
CHEMBL2047133			H-EVLF[Res_403]AEF-OH name=CHEMBL2047133
CHEMBL136752			H-{d}F{d}PR-[CTerm_423] name=CHEMBL136752
CHEMBL374725			H-HPI-OH name=CHEMBL374725
CHEMBL2347506			H-[PyGlu]PSKDAF{d}[Res_733]GLM-[NH2] name=CHEMBL2347506
CHEMBL274431			H-Y{d}RG-[CTerm_365] name=CHEMBL274431
CHEMBL2373238			H-SS{d}C(1){d}FGGRID{d}RIGA{d}QSGLG[Cys(Me)]C(1)SFR-[NH2] name=CHEMBL2373238
CHEMBL412075			H-ARYYSALRHYINLITRQRYY-OH name=CHEMBL412075
CHEMBL2070254			[NTerm_212]-GEERE[Nle]E(cyclo1)[Res_1418]{d}FRWK(cyclo1)-[NH2] name=CHEMBL2070254
CHEMBL267139			H-{d}R{d}PK{d}P{d}Q{d}Q{d}F{d}FGLM-[NH2] name=CHEMBL267139
CHEMBL414964			H-R{d}W{d}FI{d}FHKKD-[NH2] name=CHEMBL414964
CHEMBL1253457			H-KTINTSQRTIDDSNMDRNNRY-OH name=CHEMBL1253457
CHEMBL2371438			(cyclo)-[Res_699][Abu][MeGly][MeLeu]{d}V[MeGly]A{d}A{d}[MeLeu]{d}[MeLeu]{d}[MeVal]-(cyclo) name=CHEMBL2371438
CHEMBL1689455			[acetyl]-FDVC(1)KWVTLPHC(1)RVM-[NH2] name=CHEMBL1689455
CHEMBL54278			H-GGG-OH name=CHEMBL54278
CHEMBL2371455			H-[MeGly]RV{d}[Res_2141]IHPW-OH name=CHEMBL2371455
CHEMBL409908			[NTerm_1062]-[MeVal][Res_1354][Asp(pyrrol-1-yl)][Res_791][Res_2648]-OH name=CHEMBL409908
CHEMBL274428			H-Y{d}RG-[CTerm_654] name=CHEMBL274428

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.