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.

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20 randomly selected converted structures

ChEMBL ID	ChEMBL structure	Converted sequence image	Proteax PLN (Protein Line Notation)
CHEMBL2448560			(cyclo)-GVC(1)RC(2)LC(3)RRGVC(3)RC(2)LC(1)RR-(cyclo) name=CHEMBL2448560
CHEMBL374421			(cyclo)-[Res_1340]R[Res_1432]{d}YG-(cyclo) name=CHEMBL374421
CHEMBL2369449			[acetyl]-[Res_2201]RPMAS-[CTerm_326] name=CHEMBL2369449
CHEMBL1079833			[NTerm_1386]-TAE-[CTerm_810] name=CHEMBL1079833
CHEMBL436983			(cyclo)-F[MeLeu]L{d}VL-(cyclo) name=CHEMBL436983
CHEMBL3112668			H-KTNGKHMAGAA-OH name=CHEMBL3112668
CHEMBL406875			H-RPPG{d}[Res_733]SPFR-OH name=CHEMBL406875
CHEMBL432142			[acetyl]-[Res_2201][Res_989]AMAS-[CTerm_326] name=CHEMBL432142
CHEMBL1081785			[NTerm_1196]-SGS-[CTerm_789] name=CHEMBL1081785
CHEMBL2371491			H-[Res_3026](1)N{d}HRGD{d}[Res_2141]RC(1)R-OH name=CHEMBL2371491
CHEMBL2029393			H-FSR-OH name=CHEMBL2029393
CHEMBL2370697			H-YGGF{d}MA-[NH2] name=CHEMBL2370697
CHEMBL2380933			[acetyl]-WMEWDREINNYTSLIHSLKEESQNQQEKNEQELL-[NH2] name=CHEMBL2380933
CHEMBL1645526			H-[Res_2206]VL-[CTerm_208] name=CHEMBL1645526
CHEMBL2372667			H-FC(1)F{d}W{d}W{d}KT{d}F[Res_3020](1)-[NH2] name=CHEMBL2372667
CHEMBL425467			H-D{d}[Res_3018](1)[Res_2201]WKYC(1)V-OH name=CHEMBL425467
CHEMBL386568			H-{d}R{d}PK{d}P{d}Q{d}QFFGLM-[NH2] name=CHEMBL386568
CHEMBL410047			H-{d}C(1)N{d}FFWKTFTC(1)-OH name=CHEMBL410047
CHEMBL3092843			[NTerm_820]-[Res_1509]QPL-[CTerm_810] name=CHEMBL3092843
CHEMBL438460			[acetyl]-[Res_3018](1)IP{d}RG{d}D{d}[Res_2141]{d}R{d}C(1)-[NH2] name=CHEMBL438460

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.