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)
CHEMBL100604			[NTerm_283]-[Nle][Res_2552]P-OH name=CHEMBL100604
CHEMBL504765			H-{d}[Res_733]{d}[Res_733]{d}[Res_733]{d}[Res_733]-[NH2] name=CHEMBL504765
CHEMBL603948			H-RQWIWWWQWWW-[NH2] name=CHEMBL603948
CHEMBL524850			H-AARERRRKKR-OH name=CHEMBL524850
CHEMBL343516			(cyclo)-{d}PV{d}L{d}[Res_1789]D-(cyclo) name=CHEMBL343516
CHEMBL390860			H-SFRNGVGT[Res_594]MKKTSFQRAKS-OH name=CHEMBL390860
CHEMBL265891			H-RKKYKMRRK-[NH2] name=CHEMBL265891
CHEMBL1766946			H-KKP[Res_247]IL-OH name=CHEMBL1766946
CHEMBL2311690			[NTerm_820]-[Thr(tBu)][Abu][Res_2861]-[Unknown_terminal_1] name=CHEMBL2311690 inline-mod=C-terminal,[Unknown_terminal_1],H1,QkNGTRECAX9pWgC8/KgA/x5cALz8qAEAARhSAgABGg==
CHEMBL1170349			H-FRTLAR-OH name=CHEMBL1170349
CHEMBL526912			H-TPREAAAKKRV-OH name=CHEMBL526912
CHEMBL114889			H-YC(1)[Res_2201]C(1)-OH name=CHEMBL114889
CHEMBL1626412			H-AVA-[CTerm_861] name=CHEMBL1626412
CHEMBL2371995			H-ELMNS{d}[Res_895][Res_2465]GL{d}[Res_895][Res_2465]GK{d}[Res_895][Res_2465]GL{d}[Res_895][Res_2465]GK{d}[Res_895][Res_2465]ELMNS-[NH2] name=CHEMBL2371995
CHEMBL1761963			[NTerm_233]-[Res_1354][Res_2910][Res_1514]-[CTerm_1100] name=CHEMBL1761963
CHEMBL401194			[NTerm_111]-G[Res_54][Res_54][Res_54][Res_54][Res_54]-[CTerm_1225] name=CHEMBL401194
CHEMBL89736			[acetyl]-{d}FLDIIY-OH name=CHEMBL89736
CHEMBL1098991			(cyclo)-{d}P[Res_1724]V[Orn]L{d}P[Res_1724]V[Orn]L-(cyclo) name=CHEMBL1098991
CHEMBL405836			H-[MeGly]RV{d}YI{d}HPI-OH name=CHEMBL405836
CHEMBL1701696			H-RGYVYQGL-OH name=CHEMBL1701696

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.