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)
CHEMBL2369383			[NTerm_345]-WIQNW{d}PRA-[NH2] name=CHEMBL2369383
CHEMBL263185			H-HNPASFIGLM-[NH2] name=CHEMBL263185
CHEMBL421028			[acetyl]-H[Res_272]RW-[NH2] name=CHEMBL421028
CHEMBL1089576			[acetyl]-LHLGLAR-OH name=CHEMBL1089576
CHEMBL2440325			[NTerm_759]-KK[Nle]-[NH2] name=CHEMBL2440325
CHEMBL1791144			H-D{d}RVYIH{d}PF-OH name=CHEMBL1791144
CHEMBL268171			[acetyl]-RNPDGDVGGPWAYTTNPRKLYDY-[NH2] name=CHEMBL268171
CHEMBL506133			H-H{d}SDGIFTDSYSRYRKQMAVKKYLAAVL-[NH2] name=CHEMBL506133
CHEMBL160045			[NTerm_820]-V[Res_2686]V-[CTerm_707] name=CHEMBL160045
CHEMBL430081			H-YGG{d}[Res_23]LRR{d}ARPK-[NH2] name=CHEMBL430081
CHEMBL430265			H-R{d}W{d}FI{d}FHKRK-[NH2] name=CHEMBL430265
CHEMBL1938613			H-ACPI-OH name=CHEMBL1938613
CHEMBL1610363			H-[Res_1700]VP-[CTerm_980] name=CHEMBL1610363
CHEMBL1822696			(cyclo)-K[Res_2648]{d}A[Res_2648]{d}A[Res_2648]{d}A[Res_2648]-(cyclo) name=CHEMBL1822696
CHEMBL1200173			[NTerm_1451]-RPY[Res_1354]L-OH name=CHEMBL1200173
CHEMBL412730			[acetyl]-IC(1)V{d}WQ{d}DWGA{d}H[Res_164]C(1)T-OH name=CHEMBL412730
CHEMBL2369763			H-[PyGlu]QFFGLM-[NH2] name=CHEMBL2369763
CHEMBL1774121			[NTerm_178]-T[Res_2438]PR-OH name=CHEMBL1774121
CHEMBL238078			H-SLIGRL-[NH2] name=CHEMBL238078
CHEMBL267752			[acetyl]-DE[Res_1724]E[Res_2201]C-[CTerm_63] name=CHEMBL267752

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.