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)
CHEMBL430161			[acetyl]-EPQ[PhTyr]QPGQNL-[NH2] name=CHEMBL430161
CHEMBL2372352			H-DA[Res_2168]-[CTerm_810] name=CHEMBL2372352
CHEMBL2049162			H-RRRR-OH name=CHEMBL2049162
CHEMBL2370318			[acetyl]-[Res_1340][Res_1340]LRP-[CTerm_258] name=CHEMBL2370318
CHEMBL1790801			H-MNYALKGQGRTLYGF-OH name=CHEMBL1790801
CHEMBL2369492			[NTerm_958]-IFG-OH name=CHEMBL2369492
CHEMBL1814543			(cyclo)-PLKVKL{d}YPVKL{d}KV{d}Y-(cyclo) name=CHEMBL1814543
CHEMBL216533			H-DRVYIH{d}P[Hse]-OH name=CHEMBL216533
CHEMBL508239			H-[Res_254]VPAAVVVL-OH name=CHEMBL508239
CHEMBL263593			[acetyl]-{d}[Res_1340][Res_2708]{d}[Res_1340]SYRLR{d}PG-[NH2] name=CHEMBL263593
CHEMBL459207			[NTerm_590]-{d}[Res_44][MeLeu][Res_386]-[CTerm_369] name=CHEMBL459207
CHEMBL1644432			H-AEEEIYGE[Res_1612]EAKKKK-[NH2] name=CHEMBL1644432
CHEMBL1254539			[acetyl]-A[Res_2405]A-OH name=CHEMBL1254539
CHEMBL1253423			H-HIKQILINYIQECKPIQNIS-OH name=CHEMBL1253423
CHEMBL489864			[NTerm_227]-[Res_364][Res_364]F-[CTerm_855] name=CHEMBL489864
CHEMBL294814			[NTerm_700]-Q{d}FF-[CTerm_663] name=CHEMBL294814
CHEMBL506987			H-TPR[Res_1027]RRRKKRG-OH name=CHEMBL506987
CHEMBL112521			H-GPR[Res_1593]-OH name=CHEMBL112521
CHEMBL429932			[NTerm_856]-W[Res_2433]D{d}[Res_733]-[NH2] name=CHEMBL429932
CHEMBL328422			[NTerm_700]-W[Res_523]DF-[NH2] name=CHEMBL328422

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.