Structure of PDB 8ilf Chain A Binding Site BS03

Receptor Information
>8ilf Chain A (length=176) Species: 10498 (African swine fever virus BA71V) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GGMLTLIQGKKIVNHLRSRLAFEYNGQLIKILSKNIVAVGSLRREEKMLN
DVDLLIIVPEKKLLKHVLPNIRIKGLSFSVKVCGERKCVLFIEWEKKTYQ
LDLFTALAEEKPYAIFHFTGPVSYLIRIRAALKKKNYKLNQYGLFKNQTL
VPLKITTEKELIKELGFTYRIPKKRL
Ligand information
Ligand ID7Q6
InChIInChI=1S/C10H16N5O12P3Se/c11-10-13-8-7(9(17)14-10)12-3-15(8)6-1-4(16)5(25-6)2-24-30(23,31)27-29(21,22)26-28(18,19)20/h3-6,16H,1-2H2,(H,21,22)(H,23,31)(H2,18,19,20)(H3,11,13,14,17)/t4-,5+,6+,30+/m0/s1
InChIKeyUKPXRYIQPLICEM-KUFCIHQDSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1nc2c(n1C3CC(C(O3)COP(=O)(OP(=O)(O)OP(=O)(O)O)[SeH])O)N=C(NC2=O)N
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[CH]3C[CH](O)[CH](CO[P]([SeH])(=O)O[P](O)(=O)O[P](O)(O)=O)O3
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[C@H]3C[C@H](O)[C@@H](CO[P@]([SeH])(=O)O[P](O)(=O)O[P](O)(O)=O)O3
OpenEye OEToolkits 2.0.7c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)CO[P@](=O)(OP(=O)(O)OP(=O)(O)O)[SeH])O)N=C(NC2=O)N
FormulaC10 H16 N5 O12 P3 Se
Name[[(2R,3S,5R)-5-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-3-oxidanyl-oxolan-2-yl]methoxy-selanyl-phosphoryl] phosphono hydrogen phosphate
ChEMBL
DrugBank
ZINC
PDB chain8ilf Chain A Residue 202 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8ilf Structural Insight into Polymerase Mechanism via a Chiral Center Generated with a Single Selenium Atom.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		G38 S39 R42 N48 D49 D51 H115 F116 T117 G118 V120 L123 R127
Binding residue
(residue number reindexed from 1)		G40 S41 R44 N50 D51 D53 H117 F118 T119 G120 V122 L125 R129
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.7: DNA-directed DNA polymerase.
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003887 DNA-directed DNA polymerase activity
GO:0016779 nucleotidyltransferase activity
GO:0046872 metal ion binding
Biological Process
GO:0006259 DNA metabolic process
GO:0006281 DNA repair
GO:0006303 double-strand break repair via nonhomologous end joining
GO:0071897 DNA biosynthetic process
Cellular Component
GO:0044423 virion component

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8ilf, PDBe:8ilf, PDBj:8ilf
PDBsum8ilf
PubMed37958741
UniProtP42494|DPOLX_ASFB7 Repair DNA polymerase X (Gene Name=Ba71V-97)

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