Structure of PDB 1ju6 Chain D Binding Site BS03

Receptor Information
>1ju6 Chain D (length=286) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HGELQYLGQIQHILRCGVEKDDRTGTGTLSVFGMQARYSLRDEFPLLTTK
RVFWKGVLEELLWFIKGSTNAKELSSKGVKIWDANGSRDFLDSLGFSTRE
EGDLGPVYGFQWRHFGAEYRDMESDYSGQGVDQLQRVIDTIKTNPDDRRI
IMCAWNPRDLPLMALPPCHALCQFYVVNSELSCQLYQRSGDMGLGVPFNI
ASYALLTYMIAHITGLKPGDFIHTLGDAHIYLNHIEPLKIQLQREPRPFP
KLRILRKVEKIDDFKAEDFQIEGYNPHPTIKMEMAV
Ligand information
Ligand IDLYA
InChIInChI=1S/C20H21N5O6/c21-20-24-16-15(18(29)25-20)12(9-22-16)6-3-10-1-4-11(5-2-10)17(28)23-13(19(30)31)7-8-14(26)27/h1-2,4-5,9,13H,3,6-8H2,(H,23,28)(H,26,27)(H,30,31)(H4,21,22,24,25,29)/t13-/m0/s1
InChIKeyWBXPDJSOTKVWSJ-ZDUSSCGKSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC1=NC(=O)c2c(CCc3ccc(cc3)C(=O)N[CH](CCC(O)=O)C(O)=O)c[nH]c2N1
CACTVS 3.341NC1=NC(=O)c2c(CCc3ccc(cc3)C(=O)N[C@@H](CCC(O)=O)C(O)=O)c[nH]c2N1
ACDLabs 10.04O=C(O)C(NC(=O)c1ccc(cc1)CCc2cnc3NC(=NC(=O)c23)N)CCC(=O)O
OpenEye OEToolkits 1.5.0c1cc(ccc1CCc2c[nH]c3c2C(=O)N=C(N3)N)C(=O)NC(CCC(=O)O)C(=O)O
OpenEye OEToolkits 1.5.0c1cc(ccc1CCc2c[nH]c3c2C(=O)N=C(N3)N)C(=O)N[C@@H](CCC(=O)O)C(=O)O
FormulaC20 H21 N5 O6
Name2-{4-[2-(2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDIN-5-YL)-ETHYL]-BENZOYLAMINO}-PENTANEDIOIC ACID;
LY231514
ChEMBLCHEMBL225072
DrugBankDB00642
ZINCZINC000001540998
PDB chain1ju6 Chain D Residue 315 [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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PDB1ju6 Multi-targeted antifolates aimed at avoiding drug resistance form covalent closed inhibitory complexes with human and Escherichia coli thymidylate synthases.
Resolution2.89 Å
Binding residue
(original residue number in PDB)		F80 I108 L221 G222 M311 A312
Binding residue
(residue number reindexed from 1)		F53 I81 L194 G195 M284 A285
Annotation score2
Binding affinityBindingDB: IC50=9500nM,Ki=1.3nM
Enzymatic activity
Catalytic site (original residue number in PDB) E87 W109 Y135 C195 R215 D218
Catalytic site (residue number reindexed from 1) E60 W82 Y108 C168 R188 D191
Enzyme Commision number 2.1.1.45: thymidylate synthase.
Gene Ontology
Molecular Function
GO:0000900 mRNA regulatory element binding translation repressor activity
GO:0003729 mRNA binding
GO:0004799 thymidylate synthase activity
GO:0005542 folic acid binding
GO:0008168 methyltransferase activity
GO:0016741 transferase activity, transferring one-carbon groups
GO:0042803 protein homodimerization activity
GO:1901363 heterocyclic compound binding
GO:1990825 sequence-specific mRNA binding
Biological Process
GO:0006206 pyrimidine nucleobase metabolic process
GO:0006231 dTMP biosynthetic process
GO:0006235 dTTP biosynthetic process
GO:0006417 regulation of translation
GO:0007623 circadian rhythm
GO:0009165 nucleotide biosynthetic process
GO:0009410 response to xenobiotic stimulus
GO:0009636 response to toxic substance
GO:0014070 response to organic cyclic compound
GO:0017148 negative regulation of translation
GO:0019860 uracil metabolic process
GO:0032259 methylation
GO:0032570 response to progesterone
GO:0033189 response to vitamin A
GO:0034097 response to cytokine
GO:0035999 tetrahydrofolate interconversion
GO:0045471 response to ethanol
GO:0046653 tetrahydrofolate metabolic process
GO:0046683 response to organophosphorus
GO:0048589 developmental growth
GO:0051216 cartilage development
GO:0051384 response to glucocorticoid
GO:0051593 response to folic acid
GO:0060574 intestinal epithelial cell maturation
GO:0071897 DNA biosynthetic process
GO:0097421 liver regeneration
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005743 mitochondrial inner membrane
GO:0005759 mitochondrial matrix
GO:0005829 cytosol

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1ju6, PDBe:1ju6, PDBj:1ju6
PDBsum1ju6
PubMed11697906
UniProtP04818|TYSY_HUMAN Thymidylate synthase (Gene Name=TYMS)

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