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 IDChEMBL structureConverted sequence imageProteax PLN (Protein Line Notation)
CHEMBL264011H-{d}RP{d}KPQQ{d}FFG{d}LM-OH name=CHEMBL264011
CHEMBL1076111[NTerm_1338]-YHH-[CTerm_88] name=CHEMBL1076111
CHEMBL2382087[NTerm_820]-RFK-[CTerm_1072] name=CHEMBL2382087
CHEMBL505820H-ATRKGYSKF-OH name=CHEMBL505820
CHEMBL2370381[NTerm_345]-[Res_2232]FVNK{d}PRR-[NH2] name=CHEMBL2370381
CHEMBL2311114H-Y{d}AGFL-[NH2] name=CHEMBL2311114
CHEMBL590654(cyclo)-RGD{d}F[Res_1130]-(cyclo) name=CHEMBL590654
CHEMBL1915718[NTerm_621]-NQL-[Unknown_terminal_1] name=CHEMBL1915718 inline-mod=C-terminal,[Unknown_terminal_1],H1,QkNGTRECAeBsEQAAAAAAYCITAAAAAAEAARhSAgABGg==
CHEMBL2372701[NTerm_808]-KIP[Abu]-OH name=CHEMBL2372701
CHEMBL2096796[NTerm_700]-L[Res_594]VG[Res_594]VVI[Res_594]{d}[Res_1979]V[Res_594]VI[Res_594]-[CTerm_810] name=CHEMBL2096796
CHEMBL1790164[NTerm_820]-RIF-[Unknown_terminal_1] name=CHEMBL1790164 inline-mod=C-terminal,[Unknown_terminal_1],H1,QkNGTRECAf/1DwCQ/y8Af6sRAJD/LwEAARhSAgABGg==
CHEMBL2371950H-[Res_977]{d}M{d}M[Res_977]-OH name=CHEMBL2371950
CHEMBL271619H-Y{d}AGFPLW-[CTerm_1086] name=CHEMBL271619
CHEMBL2418116(cyclo)-LKKRRWKKAK{d}PPTW-(cyclo) name=CHEMBL2418116
CHEMBL2103945[acetyl]-{d}[Res_1340][Res_1788]{d}[Res_1343]S{d}Y{d}[Res_2895]L[Res_2151]P{d}A-[NH2] name=CHEMBL2103945
CHEMBL262091[NTerm_414]-{d}H{d}[Res_2713][Res_488]{d}WA-[NH2] name=CHEMBL262091
CHEMBL2368728H-{d}AELAALEAELAALEGWSPLLGRILGKLAALKAKLAALKA-OH name=CHEMBL2368728
CHEMBL290444[acetyl]-W[Res_968]DF-[NH2] name=CHEMBL290444
CHEMBL2370864[NTerm_1122]-[D-aMePhg][Res_2297]R-[Unknown_terminal_1] name=CHEMBL2370864 inline-mod=C-terminal,[Unknown_terminal_1],H1,QkNGTRECAbAFDgAHACkAMLsPAAcAKQEAARhSAgABGg==
CHEMBL2028934H-[MeGly]RVY{d}[Res_1211]HPF-OH name=CHEMBL2028934

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:

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:

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.