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)
CHEMBL2304281			(cyclo)-[MeVal][Res_799][Abu][MeGly][MeVal]V[MeLeu]A{d}A[MeLeu][MeLeu]-(cyclo) name=CHEMBL2304281
CHEMBL1097275			H-MKIPFFILHILLLQFLICLIY-OH name=CHEMBL1097275
CHEMBL499709			H-TPRDRRRKKRG-[NH2] name=CHEMBL499709
CHEMBL57082			H-FGFG-OH name=CHEMBL57082
CHEMBL506517			H-H[Res_594]DGIFTDSYSRYRKQMAVKKYLAAVLGKRYKQRVKNK-[NH2] name=CHEMBL506517
CHEMBL278824			[acetyl]-[PhTyr]EW-[NH2] name=CHEMBL278824
CHEMBL427811			H-[PyGlu]GPPISIDLPY[Res_625]LLRKMIEIEKQEKEKQQAANNRLLLDTI-OH name=CHEMBL427811
CHEMBL2335405			H-NQVANHQ-OH name=CHEMBL2335405
CHEMBL176191			[NTerm_187]-LLL-[CTerm_437] name=CHEMBL176191
CHEMBL412337			(cyclo)-[Res_2130]SG[Res_2310][Res_180][Res_2072]-(cyclo) name=CHEMBL412337
CHEMBL218433			H-[Tyr(3,5-diMe)]PW{d}[Res_1340]-[NH2] name=CHEMBL218433
CHEMBL1081049			[NTerm_801]-PGF-[CTerm_810] name=CHEMBL1081049
CHEMBL3040195			[NTerm_2]-ILG-OH name=CHEMBL3040195
CHEMBL2371786			(cyclo)-[Res_362][Abu][MeGly][MeLeu]V[MeLeu]A{d}A[MeLeu][MeLeu][MeVal]-(cyclo) name=CHEMBL2371786
CHEMBL414747			H-IKQLLHFFQRFGGGRWRRLLKKLHHLLH-[NH2] name=CHEMBL414747
CHEMBL268297			[acetyl]-{d}[Res_1340]{d}[Res_1788]{d}[Res_1343]{d}[Res_2371]{d}[Res_1357][Res_1357]L[Res_2151]P{d}A-[NH2] name=CHEMBL268297
CHEMBL1922694			H-[Res_1448]VF-[CTerm_1086] name=CHEMBL1922694
CHEMBL1808907			[NTerm_1463]-R{d}[Res_403]R-[CTerm_806] name=CHEMBL1808907
CHEMBL181003			H-AVP-[CTerm_1087] name=CHEMBL181003
CHEMBL2369681			[acetyl]-FTLDAD{d}[Res_2141]-OH name=CHEMBL2369681

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.