Structure of PDB 6npm Chain B Binding Site BS01

Receptor Information
>6npm Chain B (length=134) Species: 10377 (Human herpesvirus 4 strain B95-8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SNPKFENIAEGLRALLARSHVERTTDEGTWVAGVFVYGGSKTSLYNLRRG
TALAIPQCRLTPLSRLPFGMAPGPGPQPGPLRESIVCYFMVFLQTHIFAE
VLKDAIKDLVMTKPAPTCNIRVTVCSFDDGVDLP
Ligand information
Ligand IDKVD
InChIInChI=1S/C14H9NO2/c16-14(17)13-8-12(9-15-10-13)7-6-11-4-2-1-3-5-11/h1-5,8-10H,(H,16,17)
InChIKeyDXJZBANECHYHRT-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1ccc(cc1)C#Cc2cc(cnc2)C(=O)O
ACDLabs 12.01c1(ccccc1)C#Cc2cncc(C(O)=O)c2
CACTVS 3.385OC(=O)c1cncc(c1)C#Cc2ccccc2
FormulaC14 H9 N O2
Name5-(phenylethynyl)pyridine-3-carboxylic acid
ChEMBLCHEMBL1324612
DrugBank
ZINCZINC000000161474
PDB chain6npm Chain B Residue 701 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6npm Structure-based design of small-molecule inhibitors of EBNA1 DNA binding blocks Epstein-Barr virus latent infection and tumor growth.
Resolution1.603 Å
Binding residue
(original residue number in PDB)		N480 I481 G484 S516 N519 L582 K586 T590
Binding residue
(residue number reindexed from 1)		N7 I8 G11 S43 N46 L109 K113 T117
Annotation score1
Binding affinityMOAD: Ki=110uM
PDBbind-CN: -logKd/Ki=3.96,IC50=110uM
Enzymatic activity
Enzyme Commision number 3.1.21.-
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003700 DNA-binding transcription factor activity
Biological Process
GO:0006275 regulation of DNA replication
GO:0006355 regulation of DNA-templated transcription
GO:0045893 positive regulation of DNA-templated transcription
Cellular Component
GO:0042025 host cell nucleus

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6npm, PDBe:6npm, PDBj:6npm
PDBsum6npm
PubMed30842315
UniProtP03211|EBNA1_EBVB9 Epstein-Barr nuclear antigen 1 (Gene Name=EBNA1)

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