Structure of PDB 6nnr Chain B Binding Site BS01

Receptor Information
>6nnr Chain B (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 IDUMC
InChIInChI=1S/C9H15N2O8P/c12-5-3-8(11-2-1-7(13)10-9(11)14)19-6(5)4-18-20(15,16)17/h5-6,8,12H,1-4H2,(H,10,13,14)(H2,15,16,17)/t5-,6+,8+/m0/s1
InChIKeyWQQZADPPRABIFU-SHYZEUOFSA-N
SMILES
SoftwareSMILES
CACTVS 3.370O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2CCC(=O)NC2=O
OpenEye OEToolkits 1.7.6C1CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)O)O
ACDLabs 12.01O=P(O)(O)OCC2OC(N1C(=O)NC(=O)CC1)CC2O
CACTVS 3.370O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2CCC(=O)NC2=O
OpenEye OEToolkits 1.7.6C1CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O
FormulaC9 H15 N2 O8 P
Name2'-deoxy-5'-uridylic acid
ChEMBLCHEMBL3144338
DrugBank
ZINC
PDB chain6nnr Chain A Residue 901 [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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PDB6nnr Mg2+ binds to the surface of thymidylate synthase and affects hydride transfer at the interior active site.
Resolution1.05 Å
Binding residue
(original residue number in PDB)		R126 R127
Binding residue
(residue number reindexed from 1)		R126 R127
Annotation score2
Binding affinityPDBbind-CN: -logKd/Ki=5.07,Kd=8.5uM
Enzymatic activity
Catalytic site (original residue number in PDB) E58 W80 Y94 C146 R166 D169
Catalytic site (residue number reindexed from 1) E58 W80 Y94 C146 R166 D169
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:6nnr, PDBe:6nnr, PDBj:6nnr
PDBsum6nnr
PubMed23611499
UniProtP0A884|TYSY_ECOLI Thymidylate synthase (Gene Name=thyA)

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