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 IDChEMBL structureConverted sequence imageProteax PLN (Protein Line Notation)
CHEMBL1187583[acetyl]-[Res_1635]K{d}R[Res_2867]-[CTerm_663] name=CHEMBL1187583
CHEMBL1917058[NTerm_388]-WMDF-[NH2] name=CHEMBL1917058
CHEMBL1077557(cyclo)-PISIPLF-(cyclo) name=CHEMBL1077557
CHEMBL169799H-[N(Me)Cys]VFM-OH name=CHEMBL169799
CHEMBL2047133H-EVLF[Res_403]AEF-OH name=CHEMBL2047133
CHEMBL314165[NTerm_820]-[Res_1849]I[Tza]-[CTerm_1112] name=CHEMBL314165
CHEMBL415146H-{d}RP{d}KP{d}QQFFGLM-[NH2] name=CHEMBL415146
CHEMBL510473H-QRF{d}[Res_3018]TGHF[Res_594]GLYPCNGP-OH name=CHEMBL510473
CHEMBL2182019[NTerm_601]-ILG-[CTerm_843] name=CHEMBL2182019
CHEMBL2004617[acetyl]-[Res_1454][Res_692][Res_692]-[CTerm_240] name=CHEMBL2004617
CHEMBL376783[NTerm_700]-[Res_1354][Res_645][Res_1514]-OH name=CHEMBL376783
CHEMBL409783[acetyl]-WA[Res_594][Res_1053]L[Res_594]Q[Res_594][Res_594][Res_594]QL[Res_594]Q-[CTerm_1253] name=CHEMBL409783
CHEMBL1616139H-AV{d}P-[CTerm_994] name=CHEMBL1616139
CHEMBL1940955H-[Res_1218]V[Res_2201]-[CTerm_264] name=CHEMBL1940955
CHEMBL431912[NTerm_700]-W[Res_2433][MeGly][Res_277]-[NH2] name=CHEMBL431912
CHEMBL1170421[NTerm_700]-[Res_1354][Res_1037][Nva]-[CTerm_648] name=CHEMBL1170421
CHEMBL384517H-{d}FNF{d}FNQYV[Orn]L-[CTerm_585] name=CHEMBL384517

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:

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:

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.