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)
CHEMBL2371634			H-{d}RP[HyPro]G[Res_2944]S[Res_733]FR-OH name=CHEMBL2371634
CHEMBL1923367			H-EQEDEPEGAYFEWLE-OH name=CHEMBL1923367
CHEMBL1081766			[NTerm_1196]-SFS-[CTerm_623] name=CHEMBL1081766
CHEMBL431246			H-DEVV{d}P-[CTerm_1119] name=CHEMBL431246
CHEMBL1982128			[NTerm_700]-WWWW-[CTerm_810] name=CHEMBL1982128
CHEMBL2216757			(cyclo)-[MeLeu]V[MeLeu]A{d}A[MeLeu][MeVal][MeVal][N(Me)Bmt(E)][Abu][MeGly]-(cyclo) name=CHEMBL2216757
CHEMBL1255696			H-FIKHFIHRFSGGRWRRLLKKLHHLLH-[NH2] name=CHEMBL1255696
CHEMBL135448			H-{d}A{d}[Res_23]L-[CTerm_346] name=CHEMBL135448
CHEMBL242979			H-YPF[Res_2201]-[NH2] name=CHEMBL242979
CHEMBL266538			[acetyl]-RFMWMRRARPK-[NH2] name=CHEMBL266538
CHEMBL1689447			[acetyl]-YDIC(1)KYIRLPHC(1)RAV-[NH2] name=CHEMBL1689447
CHEMBL1824986			[NTerm_152]-QLDL{d}[Res_1092]-OH name=CHEMBL1824986
CHEMBL332180			[acetyl]-W[N(Me)Nle]DF-[NH2] name=CHEMBL332180
CHEMBL450584			H-{d}AAGAAAPGAV-[NH2] name=CHEMBL450584
CHEMBL150136			[acetyl]-V{d}F{d}L-[Unknown_terminal_1] name=CHEMBL150136 inline-mod=C-terminal,[Unknown_terminal_1],H1,QkNGTRECAc9JFgDk/qIAT/8XAOT+ogEAARhSAgABGg==
CHEMBL414594			H-RPK{d}PQ{d}QF{d}FGLM-[NH2] name=CHEMBL414594
CHEMBL503808			(cyclo)-PVKL{d}YPVKL{d}Y-(cyclo) name=CHEMBL503808
CHEMBL277277			H-TITYKF-OH name=CHEMBL277277
CHEMBL266606			H-[MeGly]{d}RVYIH{d}P{d}F-[NH2] name=CHEMBL266606
CHEMBL2369756			H-[Res_1788]C(1)[N(Me)3Pal]{d}WK{d}T{d}C(1)[Res_1340]-[NH2] name=CHEMBL2369756

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.