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)
CHEMBL3104244			H-G{d}C(1)C(2)SYPPC(1)FATNPDC(2)-[NH2] name=CHEMBL3104244
CHEMBL3038084			(cyclo)-[N(Me)Bmt(E)][Abu][Res_1854][MeLeu]V[MeLeu]A{d}A[MeLeu][MeLeu][MeVal]-(cyclo) name=CHEMBL3038084
CHEMBL2147259			[acetyl]-[Res_1343][Res_1220]FE[Res_1006]-[CTerm_1155] name=CHEMBL2147259
CHEMBL396685			H-IHVWDG-OH name=CHEMBL396685
CHEMBL409188			H-RSGPPGLQGRLQRLLQ-OH name=CHEMBL409188
CHEMBL524516			[NTerm_770]-{d}R{d}R{d}R{d}R-[NH2] name=CHEMBL524516
CHEMBL500290			[acetyl]-RASHLGLAR-[CTerm_904] name=CHEMBL500290
CHEMBL1076069			[NTerm_175]-YYY-[CTerm_716] name=CHEMBL1076069
CHEMBL605206			H-LEEWYKKTEELQKKFEEIIKKIEENNKKGEEGLKK-OH name=CHEMBL605206
CHEMBL374818			H-{d}[Res_966]P[Res_2951]F-[NH2] name=CHEMBL374818
CHEMBL524487			H-QRF[Res_3018]TGHFGGLY{d}P{d}CNGP-OH name=CHEMBL524487
CHEMBL2370413			(cyclo)-{d}[Res_44]{d}[Res_44]AA[N(Me)Tyr(Me)]A-(cyclo) name=CHEMBL2370413
CHEMBL2371899			(cyclo)-D{d}F[Res_690]RG-(cyclo) name=CHEMBL2371899
CHEMBL375688			[NTerm_700]-[Res_2713][Res_1921]W-[CTerm_1232] name=CHEMBL375688
CHEMBL1645516			H-[Res_591]SVL-[CTerm_21] name=CHEMBL1645516
CHEMBL2409067			[acetyl]-AA{d}[PhSer]PR-[CTerm_904] name=CHEMBL2409067
CHEMBL1275873			H-HRRWWRF-OH name=CHEMBL1275873
CHEMBL268829			[acetyl]-{d}[Res_1340]{d}[Res_1788][Res_1343]S{d}[Res_2785]{d}[Res_143][Res_958][Res_2151]P{d}A-[NH2] name=CHEMBL268829
CHEMBL2372568			[NTerm_579]-AAPV-[CTerm_904] name=CHEMBL2372568
CHEMBL437615			[acetyl]-[Nle]EHFRWGKP-[NH2] name=CHEMBL437615

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.