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)
CHEMBL2049013			[NTerm_923]-RVR-[CTerm_1109] name=CHEMBL2049013
CHEMBL266209			H-DRVYIH{d}PA-OH name=CHEMBL266209
CHEMBL2369790			[NTerm_283]-SY{d}LLRP-[CTerm_258] name=CHEMBL2369790
CHEMBL217327			H-{d}C(1){d}N{d}K{d}LH{d}QV{d}P{d}C(1)N-OH name=CHEMBL217327
CHEMBL1782874			H-KFW-OH name=CHEMBL1782874
CHEMBL209196			[NTerm_621]-TITFDY-OH name=CHEMBL209196
CHEMBL1790528			H-YEIYDYYV-OH name=CHEMBL1790528
CHEMBL1688610			[NTerm_1229]-ATDV-OH name=CHEMBL1688610
CHEMBL1907787			[NTerm_1422]-GGGG-[CTerm_1226] name=CHEMBL1907787
CHEMBL419909			[acetyl]-HGDS-[NH2] name=CHEMBL419909
CHEMBL309151			[NTerm_700]-WLD-[CTerm_977] name=CHEMBL309151
CHEMBL304228			H-GRGDF-OH name=CHEMBL304228
CHEMBL316925			[NTerm_700]-{d}[Res_2612][Res_2290][Res_895]{d}P-OH name=CHEMBL316925
CHEMBL411400			H-{d}FC(1){d}H{d}FR{d}W[Res_3018](1)T-[NH2] name=CHEMBL411400
CHEMBL1972145			[NTerm_700]-[Res_2498]FL-[CTerm_663] name=CHEMBL1972145
CHEMBL387086			H-DR[Res_2666]Y{d}[Res_2666]HPF-OH name=CHEMBL387086
CHEMBL2370541			H-[PyGlu]HWSY[Res_1643]LRPG-[NH2] name=CHEMBL2370541
CHEMBL1256077			H-CHLRWL-OH name=CHEMBL1256077
CHEMBL2372344			H-DA[Res_594]-[CTerm_810] name=CHEMBL2372344
CHEMBL85399			(cyclo)-{d}P{d}AV{d}DT{d}A-(cyclo) name=CHEMBL85399

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.