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.

Refresh page with an empty search box to get 100 random structures.

20 randomly selected converted structures

ChEMBL ID	ChEMBL structure	Converted sequence image	Proteax PLN (Protein Line Notation)
CHEMBL1163463			H-AGTADC(1)FWKYC(1)V-OH name=CHEMBL1163463
CHEMBL522518			H-ETDV-OH name=CHEMBL522518
CHEMBL436208			H-RVYIHP[Res_226]-OH name=CHEMBL436208
CHEMBL2370644			H-[PyGlu]HWSYKLRPG-[NH2] name=CHEMBL2370644
CHEMBL2372127			[acetyl]-IC(1)V[Res_1791]QDWGAHRC(1)T-[NH2] name=CHEMBL2372127
CHEMBL135042			[acetyl]-Q[Tyr(CH(CO2H)2)]EEIP-[NH2] name=CHEMBL135042
CHEMBL263185			H-HNPASFIGLM-[NH2] name=CHEMBL263185
CHEMBL2369492			[NTerm_958]-IFG-OH name=CHEMBL2369492
CHEMBL2311122			[acetyl]-S{d}YSMEHFRWGKPV-[NH2] name=CHEMBL2311122
CHEMBL223206			[acetyl]-PKK-[CTerm_1074] name=CHEMBL223206
CHEMBL511009			H-RWRWWIKII-OH name=CHEMBL511009
CHEMBL1076076			[NTerm_67]-YYY-[CTerm_70] name=CHEMBL1076076
CHEMBL2047131			H-EVLF{d}CAEF-OH name=CHEMBL2047131
CHEMBL507588			H-GRC(1)T{d}[Res_1276]SIPPIC(1)FPD-OH name=CHEMBL507588
CHEMBL130773			[NTerm_68]-{d}F[Phe(3-Ph)]R-[CTerm_1150] name=CHEMBL130773
CHEMBL1567081			H-VVP-[CTerm_980] name=CHEMBL1567081
CHEMBL403504			[NTerm_24]-QLTVWGIKQLQARI-OH name=CHEMBL403504
CHEMBL414384			H-DR[Res_1027]Y[Res_1027]HPF-OH name=CHEMBL414384
CHEMBL1189291			[NTerm_1115]-{d}L{d}[Res_419]{d}[Res_270]-OH name=CHEMBL1189291
CHEMBL410090			H-FC(1)YWKT{d}[Res_3018](1)T-[NH2] name=CHEMBL410090

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.