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)
CHEMBL134922			H-YGGFA-[NH2] name=CHEMBL134922
CHEMBL2409224			H-Y{d}AGFLRKYPK-OH name=CHEMBL2409224
CHEMBL119685			H-[Res_764]V{d}[Res_895]M-OH name=CHEMBL119685
CHEMBL429326			H-GRKKRRQRRRC-OH name=CHEMBL429326
CHEMBL384431			[NTerm_203]-FVR-[CTerm_1150] name=CHEMBL384431
CHEMBL1775054			[acetyl]-D(cyclo1)RWF{d}QK(cyclo1)-[NH2] name=CHEMBL1775054
CHEMBL124064			[acetyl]-[Res_2357]{d}[Res_2357]IV[Res_2471]-[CTerm_613] name=CHEMBL124064
CHEMBL1784382			(cyclo)-SV[Res_733]GV[Res_1467]V[Res_1467]V{d}[Res_1700]GV[Res_678][N(Me)aIle]-(cyclo) name=CHEMBL1784382
CHEMBL1673302			H-GIFSKLAGKKIKNLLISGLKG-[NH2] name=CHEMBL1673302
CHEMBL2372212			H-Y[Res_3018](1)FD{d}[Res_3018](1)[Nle]G-[NH2] name=CHEMBL2372212
CHEMBL72006			[NTerm_820]-LLY-[CTerm_446] name=CHEMBL72006
CHEMBL2369705			H-[aMeHis]ADAIFTSSYRRILAQLIFRKLL[His_mod2]{d}C(1)I{d}[Nle]N{d}C(1)-[NH2] name=CHEMBL2369705
CHEMBL1790304			[acetyl]-DIVPC-OH name=CHEMBL1790304
CHEMBL584800			[NTerm_1622]-YGGFLR[Res_1432]IR{d}PK-[NH2] name=CHEMBL584800
CHEMBL314602			(cyclo)-{d}P{d}A{d}[Res_245]{d}DT{d}D-(cyclo) name=CHEMBL314602
CHEMBL1178133			H-Y{d}RG-[CTerm_1205] name=CHEMBL1178133
CHEMBL405664			[NTerm_469]-VPV-[CTerm_282] name=CHEMBL405664
CHEMBL321894			H-DEVV{d}P-[CTerm_482] name=CHEMBL321894
CHEMBL2310895			H-[MeGly]RVYIHP[N(Me)hPhe]-OH name=CHEMBL2310895
CHEMBL413492			H-{d}[Res_2730]V{d}M[PhTyr]NLGE-OH name=CHEMBL413492

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.