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)
CHEMBL1076123			[NTerm_801]-LFF-[CTerm_278] name=CHEMBL1076123
CHEMBL505605			[acetyl]-SGRG[Res_1250]GGKGLGKGGAKRHRK-OH name=CHEMBL505605
CHEMBL426843			[formyl]-CV[Res_2470]M-OH name=CHEMBL426843
CHEMBL2086943			H-C(1)GRLR{d}C(1)PM-[CTerm_1160] name=CHEMBL2086943
CHEMBL1170643			H-FLT[Nle]AR-OH name=CHEMBL1170643
CHEMBL215711			H-KEHQF-OH name=CHEMBL215711
CHEMBL429765			H-VPTDVGAFAF-OH name=CHEMBL429765
CHEMBL1183130			H-[Res_2520]YIL-OH name=CHEMBL1183130
CHEMBL276454			H-Y{d}RG-[CTerm_573] name=CHEMBL276454
CHEMBL1790924			[acetyl]-LTLDADF-OH name=CHEMBL1790924
CHEMBL254919			H-{d}[Res_966]PF{d}[Res_1340]-[NH2] name=CHEMBL254919
CHEMBL261973			(cyclo)-[N(Me)Bmt(E)][Abu][MeGly][MeLeu]V[MeLeu]A[Res_786][MeLeu][MeLeu][MeVal]-(cyclo) name=CHEMBL261973
CHEMBL2369986			(cyclo)-PF[Res_2666]W{d}L-(cyclo) name=CHEMBL2369986
CHEMBL1673356			H-RRWKIVVIRWRR-[NH2] name=CHEMBL1673356
CHEMBL1206334			H-[Res_1873][Nle]GW[Nle]DF-[NH2] name=CHEMBL1206334
CHEMBL2370621			H-C(1)[Res_2232]{d}FV{d}N{d}C(1)P{d}[Res_2510]G-[NH2] name=CHEMBL2370621
CHEMBL204518			[NTerm_820]-I[Res_1485]A-[CTerm_802] name=CHEMBL204518
CHEMBL397527			[acetyl]-HYLNLVTRQRY-[NH2] name=CHEMBL397527
CHEMBL334299			H-Y{d}AYDVVG-[NH2] name=CHEMBL334299
CHEMBL136232			H-[PhTyr]MDMS-OH name=CHEMBL136232

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.