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

Search is done within records with converted sequences only. Result listing is limited to max. 100 records.

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20 randomly selected converted structures

ChEMBL ID	ChEMBL structure	Converted sequence image	Proteax PLN (Protein Line Notation)
CHEMBL2370311			[acetyl]-[Res_1340]Y[Res_1340]RA-[NH2] name=CHEMBL2370311
CHEMBL217767			[acetyl]-[Res_2511][Nle]GW[Nle]DF-[NH2] name=CHEMBL217767
CHEMBL1558517			H-[Res_1700]IP-[CTerm_717] name=CHEMBL1558517
CHEMBL1672711			H-[Res_2051]YGGFL-[NH2] name=CHEMBL1672711
CHEMBL2147245			[acetyl]-DYFG{d}[Res_1092]-[CTerm_1155] name=CHEMBL2147245
CHEMBL118138			H-VVLGVVFGI-OH name=CHEMBL118138
CHEMBL421286			H-[MeGly]AA-[CTerm_543] name=CHEMBL421286
CHEMBL1241345			[NTerm_836]-[Res_1354][Res_57][Res_1514]-OH name=CHEMBL1241345
CHEMBL2347657			H-[PyGlu]PNPDEFVGLM-[NH2] name=CHEMBL2347657
CHEMBL406532			(cyclo)-{d}P{d}ML{d}DT{d}D-(cyclo) name=CHEMBL406532
CHEMBL2013172			[NTerm_945]-[Res_1354][Res_1369][Res_2197]-OH name=CHEMBL2013172
CHEMBL436083			[NTerm_825]-C(1)R[Res_1340]{d}C(1)-[CTerm_720] name=CHEMBL436083
CHEMBL131548			[NTerm_820]-[Res_1743]VPV-[CTerm_707] name=CHEMBL131548
CHEMBL267861			[NTerm_1650]-[Res_140]GW[Res_484]D[Res_277]-[NH2] name=CHEMBL267861
CHEMBL2387215			H-{d}[Res_966]{d}AG[Res_1788]LR{d}RQF[Res_1094]-OH name=CHEMBL2387215
CHEMBL2304077			[NTerm_820]-RP[Res_1743]PQQ{d}VVGL{d}M-[CTerm_810] name=CHEMBL2304077
CHEMBL123056			[NTerm_152]-W[N(Me)Nle]DF-[NH2] name=CHEMBL123056
CHEMBL1170633			[NTerm_1034]-RPY[Res_1354]L-OH name=CHEMBL1170633
CHEMBL372874			(cyclo)-[Res_262]R[Res_1340]G{d}Y-(cyclo) name=CHEMBL372874
CHEMBL488718			[NTerm_187]-LL[Res_863]-[CTerm_373] name=CHEMBL488718

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.