Structure of PDB 4o4r Chain A Binding Site BS02

Receptor Information
>4o4r Chain A (length=476) Species: 223997 (Murine norovirus 1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RPSGTYAGLPIADYGDAPPLSTKTMFWRTSPEKLPPGAWEPAYLGSKDER
VDGPSLQQVMRDQLKPYSEPRGLLPPQEILDAVCDAIENRLENTLEPQKP
WTFKKACESLDKNTSSGYPYHKQKSKDWTGSAFIGDLGDQATHANNMYEM
GKSMRPIYTAALKDELVKPDKIYGKIKKRLLWGSDLGTMIRAARAFGPFC
DALKETCIFNPIRVGMSMNEDGPFIFARHANFRYHMDADYTRWDSTQQRA
ILKRAGDIMVRLSPEPDLARVVMDDLLAPSLLDVGDYKIVVEEGLPSGCP
CTTQLNSLAHWILTLCAMVEVTRVDPDIVMQESEFSFYGDDEVVSTNLEL
DMVKYTMALRRYGLLPTRADPLERRQTLQGISFLRRAIVGDQFGWYGRLD
RASIDRQLLWTKGPNHQNPFETLPGHAQRPSQLMALLGEAAMHGEKYYRT
VASRVSKEAAQVVPRHRSVLRWVRFG
Ligand information
Ligand ID20V
InChIInChI=1S/C18H15N4O14PS2/c1-8-17(24)13(6-23)14(7-36-37(27,28)29)18(19-8)21-20-9-2-11-12(15(3-9)38(30,31)32)4-10(22(25)26)5-16(11)39(33,34)35/h2-6,24H,7H2,1H3,(H2,27,28,29)(H,30,31,32)(H,33,34,35)/b21-20+
InChIKeyCMVLDSZYDWJTCG-QZQOTICOSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1nc(N=Nc2cc3c(cc(cc3[S](O)(=O)=O)[N+]([O-])=O)c(c2)[S](O)(=O)=O)c(CO[P](O)(O)=O)c(C=O)c1O
ACDLabs 12.01O=S(=O)(O)c3c2cc(/N=N/c1nc(c(O)c(c1COP(=O)(O)O)C=O)C)cc(c2cc([N+]([O-])=O)c3)S(=O)(=O)O
OpenEye OEToolkits 1.7.6Cc1c(c(c(c(n1)N=Nc2cc3c(cc(cc3S(=O)(=O)O)[N+](=O)[O-])c(c2)S(=O)(=O)O)COP(=O)(O)O)C=O)O
OpenEye OEToolkits 1.7.6Cc1c(c(c(c(n1)/N=N/c2cc3c(cc(cc3S(=O)(=O)O)[N+](=O)[O-])c(c2)S(=O)(=O)O)COP(=O)(O)O)C=O)O
FormulaC18 H15 N4 O14 P S2
Name3-[(E)-{4-formyl-5-hydroxy-6-methyl-3-[(phosphonooxy)methyl]pyridin-2-yl}diazenyl]-7-nitronaphthalene-1,5-disulfonic acid;
PPNDS;
Pyridoxal-5'-phosphate-6-(2'-naphthylazo-6'-nitro-4',8'-disulfonic acid)
ChEMBLCHEMBL131091
DrugBank
ZINCZINC000003995901
PDB chain4o4r Chain A Residue 602 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4o4r PPNDS inhibits murine Norovirus RNA-dependent RNA-polymerase mimicking two RNA stacking bases.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		F29 L169 Y341 R392 S410 R413 Q414
Binding residue
(residue number reindexed from 1)		F26 L166 Y338 R385 S403 R406 Q407
Annotation score1
Binding affinityMOAD: ic50=0.88uM
PDBbind-CN: -logKd/Ki=6.06,IC50=0.88uM
Enzymatic activity
Enzyme Commision number 2.7.7.48: RNA-directed RNA polymerase.
3.4.22.66: calicivirin.
3.6.1.15: nucleoside-triphosphate phosphatase.
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003968 RNA-dependent RNA polymerase activity
GO:0004386 helicase activity
GO:0005524 ATP binding
Biological Process
GO:0006351 DNA-templated transcription
GO:0039694 viral RNA genome replication

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4o4r, PDBe:4o4r, PDBj:4o4r
PDBsum4o4r
PubMed24657439
UniProtQ80J95|POLG_MNV1 Genome polyprotein (Gene Name=ORF1)

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