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)
CHEMBL1240775			H-HAEGTFTSDVSSYLEE(cyclo1)QAAK(cyclo1)EFIAWLVKGR-OH name=CHEMBL1240775
CHEMBL239163			H-R[Res_126]R-[NH2] name=CHEMBL239163
CHEMBL412685			H-DFEEIPEEYLQ-OH name=CHEMBL412685
CHEMBL2369797			(cyclo)-[Res_94]{d}F{d}W{d}K[Res_2713]{d}F-(cyclo) name=CHEMBL2369797
CHEMBL453770			H-KHAAPAAAAGA-[NH2] name=CHEMBL453770
CHEMBL108783			[NTerm_820]-VPV-[CTerm_586] name=CHEMBL108783
CHEMBL1097670			[NTerm_1145]-[MeVal][MeVal][MeVal][Res_1700]{d}[Res_733]-[CTerm_450] name=CHEMBL1097670
CHEMBL1791277			[acetyl]-HDDIIW-OH name=CHEMBL1791277
CHEMBL406769			[NTerm_965]-{d}Y{d}C(1){d}F[Res_2394]WKTFC(1)-OH name=CHEMBL406769
CHEMBL1169621			[NTerm_1439]-RPY[Res_1354]L-OH name=CHEMBL1169621
CHEMBL176842			H-{d}S{d}NVFA-[CTerm_663] name=CHEMBL176842
CHEMBL1819546			H-C(1)[Res_1791]IQNC(1)P[Res_1286]G-[NH2] name=CHEMBL1819546
CHEMBL171887			H-Y[Res_1579]FG-OH name=CHEMBL171887
CHEMBL1076663			H-[MeGly]RVY[Res_1930]HPF-OH name=CHEMBL1076663
CHEMBL1793883			H-DRVY{d}[Res_2049]H{d}PF-OH name=CHEMBL1793883
CHEMBL427057			H-TASFLLKLAGRW-[NH2] name=CHEMBL427057
CHEMBL1093606			H-RPKRPTTLNLF-OH name=CHEMBL1093606
CHEMBL1793991			(cyclo)-[Res_78][Aodo][Res_428]I-(cyclo) name=CHEMBL1793991
CHEMBL2371328			[acetyl]-{d}[Res_1510]{d}[Res_1788]{d}WSY{d}[Res_1340]LRP{d}A-[NH2] name=CHEMBL2371328
CHEMBL2372925			(cyclo)-[Res_78]{d}[Res_78]{d}FP{d}AI-(cyclo) name=CHEMBL2372925

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.