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)
CHEMBL410689			[acetyl]-MWDADDLNFTGMPPADEDYSP-[NH2] name=CHEMBL410689
CHEMBL169842			[NTerm_820]-VPV-[CTerm_1150] name=CHEMBL169842
CHEMBL249642			[acetyl]-IC(1)VVNDWGHHAC(1)T-[NH2] name=CHEMBL249642
CHEMBL1275693			[acetyl]-KWKLFKKIGKVLKKL-[NH2] name=CHEMBL1275693
CHEMBL2370136			H-RR[Res_1340]C(1)YR{d}[Res_2510]{d}KPYR{d}[Res_2510]C(1)R-OH name=CHEMBL2370136
CHEMBL3112668			H-KTNGKHMAGAA-OH name=CHEMBL3112668
CHEMBL338209			[acetyl]-[Res_2357][Res_2357]IVP[Nva]-OH name=CHEMBL338209
CHEMBL1090005			H-RPRVY{d}[Res_403][Res_1667]-[NH2] name=CHEMBL1090005
CHEMBL385700			H-R{d}PK{d}P{d}QQ{d}FFGLM-[NH2] name=CHEMBL385700
CHEMBL568577			[NTerm_1544]-H{d}F{d}R-[NH2] name=CHEMBL568577
CHEMBL2372847			[acetyl]-[Nle]DH{d}FRW[Res_1286]-[NH2] name=CHEMBL2372847
CHEMBL203990			H-G[Res_1478]E-OH name=CHEMBL203990
CHEMBL1185660			H-[Res_441]SRRARRSPRHLGSGC-OH name=CHEMBL1185660
CHEMBL246956			H-[Res_2223]GGFM-[NH2] name=CHEMBL246956
CHEMBL1966284			[NTerm_700]-[Res_2498][Res_2377]AL-[CTerm_1155] name=CHEMBL1966284
CHEMBL2372654			[NTerm_808]-KPI[Res_2179]-OH name=CHEMBL2372654
CHEMBL2371820			H-IRDECCSNPACRVNN[Res_1418]HVC-[NH2] name=CHEMBL2371820
CHEMBL1791321			[NTerm_1442]-TI[Phe(3,4-diF)]-[NH2] name=CHEMBL1791321
CHEMBL1790160			H-[MeGly]RVYIHG-[NH2] name=CHEMBL1790160
CHEMBL1688608			[NTerm_1229]-QTDV-OH name=CHEMBL1688608

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.