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)
CHEMBL2369811			(cyclo)-[Res_1701]{d}F{d}W{d}K[Res_2713]{d}F-(cyclo) name=CHEMBL2369811
CHEMBL2079563			H-{d}[Res_1340]{d}C(1)Y{d}WKVC(1)T-[NH2] name=CHEMBL2079563
CHEMBL266515			H-YGGFLRKIRPKLK-[NH2] name=CHEMBL266515
CHEMBL2371570			[acetyl]-EHWSY{d}[Res_2201]LRPG-[NH2] name=CHEMBL2371570
CHEMBL2369487			[NTerm_958]-IWG-OH name=CHEMBL2369487
CHEMBL502751			(cyclo)-PF[Res_2526]A{d}[Res_1579]AI-(cyclo) name=CHEMBL502751
CHEMBL504112			H-GQVGRQ[Nle]AIIGDDINR-OH name=CHEMBL504112
CHEMBL424081			[acetyl]-VVQA-[CTerm_707] name=CHEMBL424081
CHEMBL1796766			H-A[Res_2109]E-OH name=CHEMBL1796766
CHEMBL265198			H-GCCSNPVCHLEHSNLC-[NH2] name=CHEMBL265198
CHEMBL319684			[NTerm_859]-SLGK-[CTerm_583] name=CHEMBL319684
CHEMBL1902495			H-Y[Res_2820]GFL[Res_1771]-OH name=CHEMBL1902495
CHEMBL408811			H-YVVND[Res_2203]-OH name=CHEMBL408811
CHEMBL422461			H-GS[Res_212]FL-[NH2] name=CHEMBL422461
CHEMBL88478			[NTerm_85]-LDVP-OH name=CHEMBL88478
CHEMBL389045			H-R[Res_272]R-[CTerm_998] name=CHEMBL389045
CHEMBL264635			[NTerm_534]-[Res_2266]YN-[NH2] name=CHEMBL264635
CHEMBL1075675			[NTerm_1688]-SFQ-[CTerm_346] name=CHEMBL1075675
CHEMBL262178			[acetyl]-F[Orn]P{d}[Res_1667][Res_1092]{d}F-[NH2] name=CHEMBL262178
CHEMBL49134			H-[Res_472]AA-OH name=CHEMBL49134

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.