Structure of PDB 8pyw Chain D Binding Site BS01

Receptor Information
>8pyw Chain D (length=152) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GANLERTFIAIKPDGVQRGLVGEIIKRFEQKGFRLVAMKFLRASEEHLKQ
HYIDLKDRPFFPGLVKYMNSGPVVAMVWEGLNVVKTGRVMLGETNPADSK
PGTIRGDFCIQVGRNIIHGSDSVKSAEKEISLWFKPEELVDYKSCAHDWV
YE
Ligand information
Ligand IDIF9
InChIInChI=1S/C11H16FN5O9P2S/c1-11(12)6(18)4(2-24-28(23,29)26-27(20,21)22)25-9(11)17-3-14-5-7(17)15-10(13)16-8(5)19/h3-4,6,9,18H,2H2,1H3,(H,23,29)(H2,20,21,22)(H3,13,15,16,19)/t4-,6-,9-,11-,28+/m1/s1
InChIKeyQCBAKKHBHHSVKS-VXAAHYPFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7C[C@]1([C@@H]([C@H](O[C@H]1n2cnc3c2N=C(NC3=O)N)CO[P@@](=O)(OP(=O)(O)O)S)O)F
CACTVS 3.385C[C@@]1(F)[C@H](O)[C@@H](CO[P@@](S)(=O)O[P](O)(O)=O)O[C@H]1n2cnc3C(=O)NC(=Nc23)N
OpenEye OEToolkits 2.0.7CC1(C(C(OC1n2cnc3c2N=C(NC3=O)N)COP(=O)(OP(=O)(O)O)S)O)F
CACTVS 3.385C[C]1(F)[CH](O)[CH](CO[P](S)(=O)O[P](O)(O)=O)O[CH]1n2cnc3C(=O)NC(=Nc23)N
FormulaC11 H16 F N5 O9 P2 S
Name[[(2R,3R,4R,5R)-5-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-4-fluoranyl-4-methyl-3-oxidanyl-oxolan-2-yl]methoxy-sulfanyl-phosphoryl] dihydrogen phosphate
ChEMBL
DrugBank
ZINC
PDB chain8pyw Chain D Residue 202 [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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PDB8pyw An exonuclease-resistant chain-terminating nucleotide analogue targeting the SARS-CoV-2 replicase complex.
Resolution1.553 Å
Binding residue
(original residue number in PDB)		L59 F64 R92 T98
Binding residue
(residue number reindexed from 1)		L55 F60 R88 T94
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.13.3: histidine kinase.
2.7.4.6: nucleoside-diphosphate kinase.
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003713 transcription coactivator activity
GO:0004550 nucleoside diphosphate kinase activity
GO:0004673 protein histidine kinase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0019003 GDP binding
GO:0042802 identical protein binding
GO:0046872 metal ion binding
GO:0051880 G-quadruplex DNA binding
Biological Process
GO:0006183 GTP biosynthetic process
GO:0006228 UTP biosynthetic process
GO:0006241 CTP biosynthetic process
GO:0007155 cell adhesion
GO:0007229 integrin-mediated signaling pathway
GO:0009117 nucleotide metabolic process
GO:0009142 nucleoside triphosphate biosynthetic process
GO:0016310 phosphorylation
GO:0018106 peptidyl-histidine phosphorylation
GO:0042981 regulation of apoptotic process
GO:0043066 negative regulation of apoptotic process
GO:0045618 positive regulation of keratinocyte differentiation
GO:0045682 regulation of epidermis development
GO:0045893 positive regulation of DNA-templated transcription
GO:0045944 positive regulation of transcription by RNA polymerase II
GO:0050679 positive regulation of epithelial cell proliferation
Cellular Component
GO:0001726 ruffle
GO:0005576 extracellular region
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005925 focal adhesion
GO:0030027 lamellipodium
GO:0034774 secretory granule lumen
GO:0042995 cell projection
GO:0048471 perinuclear region of cytoplasm
GO:0070062 extracellular exosome
GO:0071944 cell periphery
GO:1904813 ficolin-1-rich granule lumen

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8pyw, PDBe:8pyw, PDBj:8pyw
PDBsum8pyw
PubMed38096103
UniProtP22392|NDKB_HUMAN Nucleoside diphosphate kinase B (Gene Name=NME2)

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