Structure of PDB 1syn Chain B Binding Site BS03

Receptor Information
>1syn Chain B (length=264) Species: 562 (Escherichia coli) [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 IDF89
InChIInChI=1S/C27H24N4O6/c1-14-29-21-7-4-16-3-2-15(10-20(16)24(21)25(34)30-14)12-28-18-5-6-19-17(11-18)13-31(26(19)35)22(27(36)37)8-9-23(32)33/h2-7,10-11,22,28H,8-9,12-13H2,1H3,(H,32,33)(H,36,37)(H,29,30,34)/t22-/m0/s1
InChIKeyBRVFNEZMTRVUGW-QFIPXVFZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC1=Nc2ccc3ccc(cc3c2C(=O)N1)CNc4ccc5c(c4)CN(C5=O)[C@@H](CCC(=O)O)C(=O)O
CACTVS 3.341CC1=Nc2ccc3ccc(CNc4ccc5c(CN([C@@H](CCC(O)=O)C(O)=O)C5=O)c4)cc3c2C(=O)N1
OpenEye OEToolkits 1.5.0CC1=Nc2ccc3ccc(cc3c2C(=O)N1)CNc4ccc5c(c4)CN(C5=O)C(CCC(=O)O)C(=O)O
CACTVS 3.341CC1=Nc2ccc3ccc(CNc4ccc5c(CN([CH](CCC(O)=O)C(O)=O)C5=O)c4)cc3c2C(=O)N1
ACDLabs 10.04O=C(O)C(N5C(=O)c1c(cc(cc1)NCc4cc3c(ccc2N=C(NC(=O)c23)C)cc4)C5)CCC(=O)O
FormulaC27 H24 N4 O6
NameS)-2-(5(((1,2-DIHYDRO-3-METHYL-1-OXOBENZO(F)QUINAZOLIN-9-YL)METHYL)AMINO)1-OXO-2-ISOINDOLINYL)GLUTARIC ACID;
FOLATE ANALOG 1843U89
ChEMBLCHEMBL169896
DrugBank
ZINCZINC000003871820
PDB chain1syn Chain B Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1syn The complex of the anti-cancer therapeutic, BW1843U89, with thymidylate synthase at 2.0 A resolution: implications for a new mode of inhibition.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		H51 S54 E58 T78 I79 W80 W83 D169 G173 F176
Binding residue
(residue number reindexed from 1)		H51 S54 E58 T78 I79 W80 W83 D169 G173 F176
Annotation score1
Binding affinityMOAD: Kd=0.1nM
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:1syn, PDBe:1syn, PDBj:1syn
PDBsum1syn
PubMed8805515
UniProtP0A884|TYSY_ECOLI Thymidylate synthase (Gene Name=thyA)

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