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)
CHEMBL506850			[acetyl]-SNWKWWPGI-[NH2] name=CHEMBL506850
CHEMBL402860			[NTerm_800]-PEPTA[Res_2161][Res_2363]EE-[NH2] name=CHEMBL402860
CHEMBL137687			(cyclo)-V{d}LW{d}E{d}A-(cyclo) name=CHEMBL137687
CHEMBL1076383			H-[PyGlu]GVC(1)C(2)GYKLC(2)[Res_2055][Res_2532]C(1)-OH name=CHEMBL1076383
CHEMBL1791382			H-TCRHAGWDQ{d}[Res_595]VCI-[CTerm_810] name=CHEMBL1791382
CHEMBL2372692			[NTerm_808]-K[HyPro]I[Abu]-OH name=CHEMBL2372692
CHEMBL1253403			H-TIINNYIDEIITTNTNIYEN-OH name=CHEMBL1253403
CHEMBL507125			H-RLARIVVIRVAR-OH name=CHEMBL507125
CHEMBL412238			[NTerm_1258]-[Nle]GW[MeLeu]DF-[NH2] name=CHEMBL412238
CHEMBL2372776			H-FD[Nle]W-[CTerm_899] name=CHEMBL2372776
CHEMBL2369364			H-R[Res_2944]{d}[Res_895]{d}[Res_2080]R-OH name=CHEMBL2369364
CHEMBL2369499			[acetyl]-HKD[Res_2201][Res_2201]IAR-OH name=CHEMBL2369499
CHEMBL1200024			[NTerm_747]-Y{d}RG-[CTerm_939] name=CHEMBL1200024
CHEMBL341751			(cyclo)-{d}PWD{d}AV-(cyclo) name=CHEMBL341751
CHEMBL1791266			H-RKKYKTRRK-[NH2] name=CHEMBL1791266
CHEMBL1926948			[acetyl]-VVIA-OH name=CHEMBL1926948
CHEMBL2369371			H-YGPFL[Nle]R-[NH2] name=CHEMBL2369371
CHEMBL510395			H-C(1){d}DG[Res_2201]GPAC(1)-[NH2] name=CHEMBL510395
CHEMBL1790527			[NTerm_579]-IV[Res_1152][Nva]-OH name=CHEMBL1790527
CHEMBL2370659			[acetyl]-CRGD[Res_3018]-[NH2] name=CHEMBL2370659

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.