Structure of PDB 5noo Chain D Binding Site BS02

Receptor Information
>5noo Chain D (length=286) Species: 6239 (Caenorhabditis elegans) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HLNQDEYKYLKQVEQILREGTRRDDTGTGTISIFGMQSKYCLRNGTIPLL
TTKRVYWKGVLEELLWFISGSTDGKLLMEKNVKIWEKNGDRAFLDNLGFT
SREEGDLGPVYGFQWRHFGAKYVDCHTDYSGQGVDQLAEVIRQIKEQPDS
RRIIMSAWNPSDLGQMVLPPCHTMCQFYVDNGELSCQLYQRSGDMGLGVP
FNLASYGLLTHMIAKVCGLKPGTLVHTLGDAHVYSNHVDALKIQLDREPY
AFPKIRFTRDVASIDDFTSDMIALDDYKCHPKIPMD
Ligand information
Ligand IDD16
InChIInChI=1S/C21H22N4O6S/c1-11-22-14-4-3-12(9-13(14)19(28)23-11)10-25(2)17-7-6-16(32-17)20(29)24-15(21(30)31)5-8-18(26)27/h3-4,6-7,9,15H,5,8,10H2,1-2H3,(H,24,29)(H,26,27)(H,30,31)(H,22,23,28)/t15-/m0/s1
InChIKeyIVTVGDXNLFLDRM-HNNXBMFYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(c3sc(N(C)Cc2ccc1NC(=NC(=O)c1c2)C)cc3)NC(C(=O)O)CCC(=O)O
CACTVS 3.370CN(Cc1ccc2NC(=NC(=O)c2c1)C)c3sc(cc3)C(=O)N[CH](CCC(O)=O)C(O)=O
OpenEye OEToolkits 1.7.6CC1=NC(=O)c2cc(ccc2N1)CN(C)c3ccc(s3)C(=O)N[C@@H](CCC(=O)O)C(=O)O
CACTVS 3.370CN(Cc1ccc2NC(=NC(=O)c2c1)C)c3sc(cc3)C(=O)N[C@@H](CCC(O)=O)C(O)=O
OpenEye OEToolkits 1.7.6CC1=NC(=O)c2cc(ccc2N1)CN(C)c3ccc(s3)C(=O)NC(CCC(=O)O)C(=O)O
FormulaC21 H22 N4 O6 S
NameTOMUDEX;
ZD1694;
Raltitrexed
ChEMBLCHEMBL225071
DrugBankDB00293
ZINCZINC000003832372
PDB chain5noo Chain D Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5noo Crystal structures of nematode (parasitic T. spiralis and free living C. elegans), compared to mammalian, thymidylate synthases (TS). Molecular docking and molecular dynamics simulations in search for nematode-specific inhibitors of TS.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		R80 Y82 I110 D220 L223 G224 F227 Y260
Binding residue
(residue number reindexed from 1)		R54 Y56 I84 D194 L197 G198 F201 Y234
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) E89 W111 Y137 C197 R217 D220
Catalytic site (residue number reindexed from 1) E63 W85 Y111 C171 R191 D194
Enzyme Commision number 2.1.1.45: thymidylate synthase.
Gene Ontology
Molecular Function
GO:0004799 thymidylate synthase activity
GO:0008168 methyltransferase activity
GO:0016741 transferase activity, transferring one-carbon groups
Biological Process
GO:0006231 dTMP biosynthetic process
GO:0006235 dTTP biosynthetic process
GO:0009165 nucleotide biosynthetic process
GO:0032259 methylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5noo, PDBe:5noo, PDBj:5noo
PDBsum5noo
PubMed28826032
UniProtQ9Y052

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