Structure of PDB 4isk Chain F Binding Site BS03

Receptor Information
>4isk Chain F (length=264) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKQYLELMQKVLDEGTQKNDRTGTGTLSIFGHQMRFNLQDGFPLVTTKRC
HLRSIIHELLWFLQGDTNIAYLHENNVTIWDEWADENGDLGPVYGKQWRA
WPTPDGRHIDQITTVLNQLKNDPDSRRIIVSAWNVGELDKMALAPCHAFF
QFYVADGKLSCQLYQRSCDVFLGLPFNIASYALLVHMMAQQCDLEVGDFV
WTGGDTHLYSNHMDQTHLQLSREPRPLPKLIIKRKPESIFDYRFEDFEIE
GYDPHPGIKAPVAI
Ligand information
Ligand ID1JY
InChIInChI=1S/C32H33N5O10/c1-2-13-37(25-10-5-18-14-24-21(15-20(18)25)30(43)36-26(16-38)33-24)19-6-3-17(4-7-19)29(42)35-23(32(46)47)8-11-27(39)34-22(31(44)45)9-12-28(40)41/h1,3-4,6-7,14-15,22-23,25,38H,5,8-13,16H2,(H,34,39)(H,35,42)(H,40,41)(H,44,45)(H,46,47)(H,33,36,43)/t22-,23+,25+/m1/s1
InChIKeyNVHRBQOZEMFKLD-CUYJMHBOSA-N
SMILES
SoftwareSMILES
CACTVS 3.370OCC1=NC(=O)c2cc3[CH](CCc3cc2N1)N(CC#C)c4ccc(cc4)C(=O)N[CH](CCC(=O)N[CH](CCC(O)=O)C(O)=O)C(O)=O
CACTVS 3.370OCC1=NC(=O)c2cc3[C@H](CCc3cc2N1)N(CC#C)c4ccc(cc4)C(=O)N[C@@H](CCC(=O)N[C@H](CCC(O)=O)C(O)=O)C(O)=O
OpenEye OEToolkits 1.7.6C#CCN(c1ccc(cc1)C(=O)N[C@@H](CCC(=O)N[C@H](CCC(=O)O)C(=O)O)C(=O)O)[C@H]2CCc3c2cc4c(c3)NC(=NC4=O)CO
ACDLabs 12.01O=C(O)C(NC(=O)CCC(C(=O)O)NC(=O)c1ccc(cc1)N(CC#C)C4c3c(cc2c(C(=O)N=C(N2)CO)c3)CC4)CCC(=O)O
OpenEye OEToolkits 1.7.6C#CCN(c1ccc(cc1)C(=O)NC(CCC(=O)NC(CCC(=O)O)C(=O)O)C(=O)O)C2CCc3c2cc4c(c3)NC(=NC4=O)CO
FormulaC32 H33 N5 O10
NameN-(4-{[(6S)-2-(hydroxymethyl)-4-oxo-4,6,7,8-tetrahydro-1H-cyclopenta[g]quinazolin-6-yl](prop-2-yn-1-yl)amino}benzoyl)-L-gamma-glutamyl-D-glutamic acid
ChEMBLCHEMBL4594449
DrugBank
ZINC
PDB chain4isk Chain F Residue 302 [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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PDB4isk Development and Binding Mode Assessment of N-[4-[2-Propyn-1-yl[(6S)-4,6,7,8-tetrahydro-2-(hydroxymethyl)-4-oxo-3H-cyclopenta[g]quinazolin-6-yl]amino]benzoyl]-l-gamma-glutamyl-d-glutamic Acid (BGC 945), a Novel Thymidylate Synthase Inhibitor That Targets Tumor Cells.
Resolution1.752 Å
Binding residue
(original residue number in PDB)		H51 I79 W83 D169 L172 G173 F176 N177 Y209 V262 A263
Binding residue
(residue number reindexed from 1)		H51 I79 W83 D169 L172 G173 F176 N177 Y209 V262 A263
Annotation score1
Binding affinityMOAD: Ki=1.2nM
Enzymatic activity
Catalytic site (original residue number in PDB) E58 W80 Y94 C146 R166 D169 P175
Catalytic site (residue number reindexed from 1) E58 W80 Y94 C146 R166 D169 P175
Enzyme Commision number 2.1.1.45: thymidylate synthase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003723 RNA binding
GO:0004799 thymidylate synthase activity
GO:0008168 methyltransferase activity
GO:0016741 transferase activity, transferring one-carbon groups
GO:0042803 protein homodimerization activity
Biological Process
GO:0006231 dTMP biosynthetic process
GO:0006235 dTTP biosynthetic process
GO:0006417 regulation of translation
GO:0009165 nucleotide biosynthetic process
GO:0009314 response to radiation
GO:0032259 methylation
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4isk, PDBe:4isk, PDBj:4isk
PDBsum4isk
PubMed23710599
UniProtP0A884|TYSY_ECOLI Thymidylate synthase (Gene Name=thyA)

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