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)
CHEMBL2370157			H-{d}RRP{d}[Res_1508]G{d}[Res_1199]S[Res_400]{d}[Res_2080]R-OH name=CHEMBL2370157
CHEMBL1221522			H-YMG-OH name=CHEMBL1221522
CHEMBL2371634			H-{d}RP[HyPro]G[Res_2944]S[Res_733]FR-OH name=CHEMBL2371634
CHEMBL265398			H-{d}FPF{d}FNQYN[Orn]L-[CTerm_585] name=CHEMBL265398
CHEMBL324219			[NTerm_579]-W[Res_2433]D{d}[Res_733]-[NH2] name=CHEMBL324219
CHEMBL258296			H-{d}RGR-[CTerm_1150] name=CHEMBL258296
CHEMBL2336576			H-AWLAYPGAVSYR-OH name=CHEMBL2336576
CHEMBL2369676			[acetyl]-FTLDADQ-OH name=CHEMBL2369676
CHEMBL2087391			[acetyl]-{d}C(1)[Res_510]PRLRGC(1)-[NH2] name=CHEMBL2087391
CHEMBL349056			[acetyl]-{d}C(1)[Res_1432]G{d}D[Res_3018](1)-[NH2] name=CHEMBL349056
CHEMBL1080314			[NTerm_1688]-AFQ-[CTerm_373] name=CHEMBL1080314
CHEMBL273655			H-KKYIKVFVFK-[NH2] name=CHEMBL273655
CHEMBL7363			[NTerm_672]-F{d}LF{d}LF-OH name=CHEMBL7363
CHEMBL2371404			H-DRVYI[Res_920]PF-OH name=CHEMBL2371404
CHEMBL1835320			[acetyl]-VDV[Res_2784]-[CTerm_1229] name=CHEMBL1835320
CHEMBL450584			H-{d}AAGAAAPGAV-[NH2] name=CHEMBL450584
CHEMBL2380710			H-WKSYVRRWRS-OH name=CHEMBL2380710
CHEMBL1186144			[acetyl]-[Res_1544]K{d}R[Res_2867]-[CTerm_663] name=CHEMBL1186144
CHEMBL1791374			[acetyl]-CI[Res_1593]KYY-OH name=CHEMBL1791374
CHEMBL339122			H-[Res_733]PR-[CTerm_828] name=CHEMBL339122

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.