Structure of PDB 4o4r Chain A Binding Site BS01

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 601 [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)		M219 L391 R392 R393 Q414 K419
Binding residue
(residue number reindexed from 1)		M216 L384 R385 R386 Q407 K412
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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