Structure of PDB 8pyw Chain B Binding Site BS01

Receptor Information
>8pyw Chain B (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 B Residue 202 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
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 R62 F64 T98 V116
Binding residue
(residue number reindexed from 1)		L55 R58 F60 T94 V112
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

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

[Back to BioLiP]