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)
CHEMBL1077139			(cyclo)-P{d}[Res_23]FLIILVP-(cyclo) name=CHEMBL1077139
CHEMBL109659			[NTerm_1663]-AGFL-[NH2] name=CHEMBL109659
CHEMBL1630200			[acetyl]-PVLDE{d}[Res_2641]REKLNE{d}[Res_2641]LEALKQKLK-[NH2] name=CHEMBL1630200
CHEMBL1965186			[NTerm_820]-VV[MeLeu]PP-[CTerm_524] name=CHEMBL1965186
CHEMBL405254			[NTerm_579]-YEPIPEEA[Phe(4-NHSO3H)]E-OH name=CHEMBL405254
CHEMBL1632440			[acetyl]-PVLDEFREKLNE[Res_2789]LEALKQKLK-[NH2] name=CHEMBL1632440
CHEMBL252699			[NTerm_800]-PEPTA[Res_2161][Res_1265]EE-[NH2] name=CHEMBL252699
CHEMBL262497			[NTerm_820]-{d}H{d}[Res_2713]F{d}WA-[NH2] name=CHEMBL262497
CHEMBL412240			H-{d}R{d}PKP{d}Q{d}QFFGLM-[NH2] name=CHEMBL412240
CHEMBL1630199			[acetyl]-PVLDE[Res_604]REKLNE[Res_604]LEALKQKLK-[NH2] name=CHEMBL1630199
CHEMBL2370702			(cyclo)-{d}WFGL{d}MQ-(cyclo) name=CHEMBL2370702
CHEMBL411400			H-{d}FC(1){d}H{d}FR{d}W[Res_3018](1)T-[NH2] name=CHEMBL411400
CHEMBL2087402			[acetyl]-{d}[Res_3018](1)M{d}[Res_78]RLRGC(1)-[NH2] name=CHEMBL2087402
CHEMBL2371218			[NTerm_1281]-H{d}[Res_1340]RWG-[NH2] name=CHEMBL2371218
CHEMBL503808			(cyclo)-PVKL{d}YPVKL{d}Y-(cyclo) name=CHEMBL503808
CHEMBL2372166			H-RPPGFSPDR-OH name=CHEMBL2372166
CHEMBL2086573			[acetyl]-{d}C(1)M[Res_510]RLR[MeGly]C(1)-[NH2] name=CHEMBL2086573
CHEMBL1160884			H-[MeGly]RV[Res_2240]VH{d}PF-OH name=CHEMBL1160884
CHEMBL611217			H-PVLDEFREKLNE[Res_594]LE[Res_594]LKQKLK-OH name=CHEMBL611217
CHEMBL448672			H-GQVGRQLAI[Res_1593]GDDINR-OH name=CHEMBL448672

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.