Structure of PDB 8hyk Chain A Binding Site BS01

Receptor Information
>8hyk Chain A (length=306) Species: 1151187 (Enterococcus faecalis EnGen0062) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SKFSESTLSGWTKPASVTEEDRIENTISMIKSAIKNDNNFDNLVYEVFVQ
GSYGNNTNVRTNSDIDVNIMLTSTFYSKYPEGKTNSDYGFTDGTITYNEY
KNLILTALTNKFGTGNVTVGNKSIKITSNSYRVEADCIPSLLYRNYEYEN
SSSPNNYIEGIKYFASDNTSVVNYPKVHINNGIEKNNQTHKNYKRLVRVI
KRLRNKMTAENHFTNENITSFLIECLIWNVPNNYINDYDTWDETIKQTLI
FIKSSINDNSYKNWTEVSGMFYLFHNNRKWTSDDVSSFVNSLWSFMEYLE
HHHHHH
Ligand information
Ligand IDNE0
InChIInChI=1S/C9H16N2O18P4/c12-5-1-2-11(9(14)10-5)8-7(27-30(15,16)17)6(13)4(26-8)3-25-32(21,22)29-33(23,24)28-31(18,19)20/h1-2,4,6-8,13H,3H2,(H,21,22)(H,23,24)(H,10,12,14)(H2,15,16,17)(H2,18,19,20)/t4-,6-,7-,8-/m1/s1
InChIKeyOATQDFNIQGUFQP-XVFCMESISA-N
SMILES
SoftwareSMILES
CACTVS 3.385O[CH]1[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O[CH]([CH]1O[P](O)(O)=O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 2.0.7C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)OP(=O)(O)O
OpenEye OEToolkits 2.0.7C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)OP(=O)(O)O
CACTVS 3.385O[C@@H]1[C@@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O[C@H]([C@@H]1O[P](O)(O)=O)N2C=CC(=O)NC2=O
FormulaC9 H16 N2 O18 P4
Name[[(2R,3R,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-4-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate
ChEMBL
DrugBank
ZINC
PDB chain8hyk Chain A Residue 401 [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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PDB8hyk Crystal structure and functional implications of cyclic di-pyrimidine-synthesizing cGAS/DncV-like nucleotidyltransferases.
Resolution2.021 Å
Binding residue
(original residue number in PDB)
G52 S53 D67 K123 N174 F222
Binding residue
(residue number reindexed from 1)
G51 S52 D66 K122 N173 F221
Annotation score3
Enzymatic activity
Enzyme Commision number 2.7.7.-
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0016779 nucleotidyltransferase activity
GO:0046872 metal ion binding
Biological Process
GO:0009117 nucleotide metabolic process
GO:0051607 defense response to virus

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Molecular Function

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Biological Process
External links
PDB RCSB:8hyk, PDBe:8hyk, PDBj:8hyk
PDBsum8hyk
PubMed37604815
UniProtP0DX98|CDNE_ENTF2 Cyclic dipyrimidine nucleotide synthase CdnE (Gene Name=cdnE)

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