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

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20 randomly selected converted structures

ChEMBL ID	ChEMBL structure	Converted sequence image	Proteax PLN (Protein Line Notation)
CHEMBL429939			H-FGGFTGARKSARKLANQ-OH name=CHEMBL429939
CHEMBL364157			H-GVPFY-OH name=CHEMBL364157
CHEMBL268719			[NTerm_700]-[Res_607]PF[Res_111]-[CTerm_322] name=CHEMBL268719
CHEMBL1800261			H-R[Res_403]R[Nva]Y{d}[Res_403][Res_1667]-[NH2] name=CHEMBL1800261
CHEMBL572542			H-[Res_372]{d}[Res_895]FF-OH name=CHEMBL572542
CHEMBL1170645			H-FLT{d}[Res_2201]AR-OH name=CHEMBL1170645
CHEMBL350585			[NTerm_415]-VVNDL-OH name=CHEMBL350585
CHEMBL132776			H-YGGFLS-[NH2] name=CHEMBL132776
CHEMBL1091368			[NTerm_1652]-{d}K{d}R{d}[Res_2867]-[CTerm_663] name=CHEMBL1091368
CHEMBL68233			[NTerm_541]-VLS-OH name=CHEMBL68233
CHEMBL327590			H-{d}[Res_1341]LDIIW-OH name=CHEMBL327590
CHEMBL366979			H-{d}FPFCNQYV[Orn]L-[CTerm_585] name=CHEMBL366979
CHEMBL505501			H-QRF[Res_3018]TGH[Res_625]GGLYP{d}CNGP-OH name=CHEMBL505501
CHEMBL1922695			H-[Res_2467]VF-[CTerm_1086] name=CHEMBL1922695
CHEMBL274432			H-Y{d}RG-[CTerm_53] name=CHEMBL274432
CHEMBL2018416			[acetyl]-[Res_594]NII[Res_594]PLL[Res_594]PI[Res_695]-[NH2] name=CHEMBL2018416
CHEMBL2418116			(cyclo)-LKKRRWKKAK{d}PPTW-(cyclo) name=CHEMBL2418116
CHEMBL526502			H-TPRTRRRKKRG-OH name=CHEMBL526502
CHEMBL2369681			[acetyl]-FTLDAD{d}[Res_2141]-OH name=CHEMBL2369681
CHEMBL258221			H-KKPYIL-OH name=CHEMBL258221

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.