Structure of PDB 6ld2 Chain A Binding Site BS03

Receptor Information
>6ld2 Chain A (length=565) Species: 2043570 (Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PNMKIIGNRIERIRSEHAETWFFDENHPYRTWAYHGSYEAPLINGVVRLL
SKPWDVVTGVTGIAGQQRVFKEKVDTRVPDPQEGTRQVMSMVSSWLWKEL
GKHKRPRVCTKEEFINKVRSEAVNDPRFWALVDKEREHHLRGECQSCVYN
MMGRAIWYMWLGARFLEFEALGFLNEDHWMGRENSGGGVEGLGLQRLGYV
LEEMSRIPGGRMYADDTAGWDTRISRFDLENEALITNQMEKGHRALALAI
IKYTYQNKVVKVLRKGKTVMDIISRQDQRGSGQVVTYALNTFTNLVVQLI
RNMEAEEVLEMQDLWLLRRSEKVTNWLQSNGWDRLKRMAVSGDDCVVKPI
DDRFAHALRFLNDMGKVRKDTQEWKPSTGWDNWEEVPFCSHHFNKLHLKD
GRSIVVPCRHQDELIGRARVSPGAGWSIRETACLAKSYAQMWQLLYFHRR
DLRLMANAICSSVPVDWVPTGRTTWSIHGKGEWMTTEDMLVVWNRVWIEE
NDHMEDKTPVTKWTDIPYLGKREDLWCGSLIGHRPRTTWAENIKNTVNMV
RRIIGDEEKYMDYLS
Ligand information
Ligand IDKY3
InChIInChI=1S/C13H18O4S/c1-16-10-7-11(17-2)9(13(14)15)6-8(10)12-4-3-5-18-12/h3-5,8-11H,6-7H2,1-2H3,(H,14,15)/t8-,9+,10+,11+/m1/s1
InChIKeyRFIIEINMNPNZEZ-RCWTZXSCSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CO[CH]1C[CH](OC)[CH](C[CH]1C(O)=O)c2sccc2
OpenEye OEToolkits 2.0.7CO[C@H]1C[C@@H]([C@H](C[C@H]1c2cccs2)C(=O)O)OC
CACTVS 3.385CO[C@H]1C[C@H](OC)[C@@H](C[C@@H]1C(O)=O)c2sccc2
OpenEye OEToolkits 2.0.7COC1CC(C(CC1c2cccs2)C(=O)O)OC
FormulaC13 H18 O4 S
Name(1S,2S,4S,5R)-2,4-dimethoxy-5-thiophen-2-yl-cyclohexane-1-carboxylic acid
ChEMBL
DrugBank
ZINC
PDB chain6ld2 Chain A Residue 903 [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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PDB6ld2 Non-nucleoside Inhibitors of Zika Virus RNA-Dependent RNA Polymerase.
Resolution1.4 Å
Binding residue
(original residue number in PDB)
L513 C711 S712 H713 R731 M763 L767 T796 S798 H800 G801 W805
Binding residue
(residue number reindexed from 1)
L194 C389 S390 H391 R409 M441 L445 T474 S476 H478 G479 W483
Annotation score1
Binding affinityMOAD: ic50=246.6uM
Enzymatic activity
Enzyme Commision number 2.1.1.56: mRNA (guanine-N(7))-methyltransferase.
2.1.1.57: methyltransferase cap1.
2.7.7.48: RNA-directed RNA polymerase.
3.4.21.91: flavivirin.
3.6.1.15: nucleoside-triphosphate phosphatase.
3.6.4.13: RNA helicase.
Gene Ontology
Molecular Function
GO:0003968 RNA-dependent RNA polymerase activity
GO:0005524 ATP binding
Biological Process
GO:0039694 viral RNA genome replication

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Molecular Function

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Biological Process
External links
PDB RCSB:6ld2, PDBe:6ld2, PDBj:6ld2
PDBsum6ld2
PubMed32796069
UniProtA0A024B7W1|POLG_ZIKVF Genome polyprotein

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