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)
CHEMBL509512			H-GS[Res_279]FLSPEHQRVQQRKESKKPPAKLQPR-OH name=CHEMBL509512
CHEMBL1163477			[acetyl]-C(1)F{d}WKYC(1)-[NH2] name=CHEMBL1163477
CHEMBL132352			H-YGGGF-OH name=CHEMBL132352
CHEMBL1199923			[NTerm_1400]-{d}K{d}RA-[CTerm_663] name=CHEMBL1199923
CHEMBL3104468			H-AC(1)F{d}[Res_1071][Orn]YC(1)V-OH name=CHEMBL3104468
CHEMBL113012			[NTerm_820]-VAD-[CTerm_872] name=CHEMBL113012
CHEMBL441199			H-GPGGPA-[CTerm_723] name=CHEMBL441199
CHEMBL1739476			H-AV[Res_2131]-[CTerm_994] name=CHEMBL1739476
CHEMBL406474			[acetyl]-HWAVGH-[CTerm_1024] name=CHEMBL406474
CHEMBL409456			H-MTLIGAAHNGSAQLLRQLRGQLGPPGSA-[NH2] name=CHEMBL409456
CHEMBL420318			H-LFQPQRF-[NH2] name=CHEMBL420318
CHEMBL402250			(cyclo)-S[Res_801]FV-(cyclo) name=CHEMBL402250
CHEMBL131552			[NTerm_887]-F{d}AP-OH name=CHEMBL131552
CHEMBL527436			H-HSDGI[Res_2614]TDSYSRYRKQMAVKKYLAAVLGKRYKQRVKNK-[NH2] name=CHEMBL527436
CHEMBL1121			H-D[Res_1873]MGWMDF-[NH2] name=CHEMBL1121
CHEMBL2371503			[acetyl]-C(1){d}NP{d}RG{d}D{d}[Res_2141]{d}[Res_2510]C(1)-[NH2] name=CHEMBL2371503
CHEMBL407365			(cyclo)-[Res_1479]SG[Res_2310][Res_1061][Res_1723]-(cyclo) name=CHEMBL407365
CHEMBL386285			H-[Res_2533][Res_2533][Res_1390]QQQQQQQQ-[NH2] name=CHEMBL386285
CHEMBL430065			H-FLLSLGIHL-OH name=CHEMBL430065
CHEMBL150620			[NTerm_820]-L{d}F{d}L-[Unknown_terminal_1] name=CHEMBL150620 inline-mod=C-terminal,[Unknown_terminal_1],H1,QkNGTRECAc9JFgAN/6YAT/8XAA3/pgEAARhSAgABGg==

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.