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)
CHEMBL66929			[acetyl]-KPV-[NH2] name=CHEMBL66929
CHEMBL502093			[acetyl]-H[Res_2983]RW-[NH2] name=CHEMBL502093
CHEMBL415558			[NTerm_800]-PEPTA[Res_2161][Res_1278]EE-[NH2] name=CHEMBL415558
CHEMBL2375168			H-SSC(1)FG{d}[Res_3014]RIDRIGAQ{d}[Res_3014]GLGC(1)NSFR-[NH2] name=CHEMBL2375168
CHEMBL2372384			H-W{d}[Res_895]A-OH name=CHEMBL2372384
CHEMBL414341			[NTerm_36]-R[Res_78]GSGSGSGSGDFEEIPEEYLQ-OH name=CHEMBL414341
CHEMBL569220			[NTerm_971]-H{d}F{d}R-[NH2] name=CHEMBL569220
CHEMBL450156			[acetyl]-SNWKWWPGIFA-[NH2] name=CHEMBL450156
CHEMBL2316449			[NTerm_828]-VLH-[CTerm_1150] name=CHEMBL2316449
CHEMBL266089			[NTerm_1456]-MLF-OH name=CHEMBL266089
CHEMBL101345			[NTerm_855]-[Res_1354][Asp(pyrrol-1-yl)]AL-OH name=CHEMBL101345
CHEMBL1986115			[NTerm_700]-{d}V{d}[Res_733][Res_2229][Res_2229]{d}P-[CTerm_663] name=CHEMBL1986115
CHEMBL1668837			H-GGAP-[CTerm_1156] name=CHEMBL1668837
CHEMBL2370189			[acetyl]-D{d}DIVP{d}[Nva]-[CTerm_1086] name=CHEMBL2370189
CHEMBL380726			H-KPW[Res_1354]L-OH name=CHEMBL380726
CHEMBL527083			[NTerm_1208]-GRKKRRQRRRPPQ-OH name=CHEMBL527083
CHEMBL1271575			H-FRK-OH name=CHEMBL1271575
CHEMBL263697			[acetyl]-DTEDVV{d}P-[CTerm_643] name=CHEMBL263697
CHEMBL1720283			[NTerm_590]-[N(Me)Tyr(Me)][MeLeu][Res_386]-[CTerm_574] name=CHEMBL1720283
CHEMBL322110			H-DEVV{d}P-[CTerm_1153] name=CHEMBL322110

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.