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)
CHEMBL1689449			[acetyl]-FMVC(1)NYVTLPWC(1)PMQ-[NH2] name=CHEMBL1689449
CHEMBL508704			H-QRFETGHFGGLYPKNGP-OH name=CHEMBL508704
CHEMBL219285			H-REIAKK[Res_3014]R-OH name=CHEMBL219285
CHEMBL265891			H-RKKYKMRRK-[NH2] name=CHEMBL265891
CHEMBL320509			H-HCKFWW-[NH2] name=CHEMBL320509
CHEMBL169054			[NTerm_700]-W[Nle]DF-[NH2] name=CHEMBL169054
CHEMBL2371352			[acetyl]-{d}[Res_1340]{d}[Res_1788]{d}WSY{d}[Res_1510]WRP{d}A-[NH2] name=CHEMBL2371352
CHEMBL591900			[NTerm_1622]-G[Res_1895][Res_2558][Res_2558][Res_1895][Res_2558]-OH name=CHEMBL591900
CHEMBL31621			[NTerm_1362]-F[Gly(CO2Me)][Res_2201]-[CTerm_170] name=CHEMBL31621
CHEMBL437180			(cyclo)-[Res_3014](1)TKSIPPIC(1)F{d}PDGR-(cyclo) name=CHEMBL437180
CHEMBL254371			H-{d}C(1)YIQNC(1)PLG-[CTerm_293] name=CHEMBL254371
CHEMBL1793923			H-YA{d}DAIFT{d}NSYRKVLGQLSARKLLQDIISR-[NH2] name=CHEMBL1793923
CHEMBL1185881			[acetyl]-{d}[HyPro]SS[Res_2937]QSL-[CTerm_686] name=CHEMBL1185881
CHEMBL406616			H-{d}RP{d}K{d}P{d}Q{d}Q{d}F{d}FG{d}LM-[NH2] name=CHEMBL406616
CHEMBL216638			H-CY[Res_1053]VNCPRG-[NH2] name=CHEMBL216638
CHEMBL2152057			H-YNWNSFGL[Res_590]F-[NH2] name=CHEMBL2152057
CHEMBL608125			(cyclo)-FPV[Orn]L{d}[Res_945]PV[Orn]L-(cyclo) name=CHEMBL608125
CHEMBL525039			[acetyl]-WVTH{d}[Res_2510]LAGLLS{d}[Res_2510]SGGVV[Res_141]KNFVPTDVGPFAF-[NH2] name=CHEMBL525039
CHEMBL524861			[acetyl]-[Nle]D(cyclo1)[Res_262]{d}FRWK(cyclo1)-[NH2] name=CHEMBL524861
CHEMBL1790661			[NTerm_700]-F[Res_305]IV-[CTerm_810] name=CHEMBL1790661

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.