Structure of PDB 4lq3 Chain A Binding Site BS03

Receptor Information
>4lq3 Chain A (length=495) Species: 142786 (Norovirus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GTYCGAPILGPGSAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKG
GPSLQQVMRDQLKPFTEPRGKPPKPSVLEAAKKTIINVLEQTIDPPEKWS
FTQACASLDKTTSSGHPHHMRKNDCWNGESFTGKLADQASKANLMFEGGK
NMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDLATMIRCARAFGGLMDE
LKAHCVTLPIRVGMNMNEDGPIIFERHSRYKYHYDADYSRWDSTQQRAVL
AAALEIMVKFSSEPHLAQVVAEDLLSPSVVDVGDFKISINEPSGVPCTSQ
WNSIAHWLLTLCALSEVTNLSPDIIQANSLFSFYGDDEIVSTDIKLDPEK
LTAKLKEYGLKPTRPDGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSS
ILRQMYWTRGPNHEDPSETMSQRPIQLMSLLGEAALHGPAFYSKISKLVI
AELKEGMDYVPRQEPMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE
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 chain4lq3 Chain A Residue 603 [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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PDB4lq3 Naphthalene-sulfonate inhibitors of human norovirus RNA-dependent RNA-polymerase.
Resolution2.6 Å
Binding residue
(original residue number in PDB)		K166 E168 R392 L406 S410 I411 Q414 R419 D507 E510
Binding residue
(residue number reindexed from 1)		K161 E163 R382 L396 S400 I401 Q404 R409 D492 E495
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.35,IC50=0.45uM
Enzymatic activity
Enzyme Commision number 3.6.1.15: nucleoside-triphosphate phosphatase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003723 RNA binding
GO:0003968 RNA-dependent RNA polymerase activity
GO:0004386 helicase activity
GO:0005524 ATP binding
GO:0046872 metal ion binding
Biological Process
GO:0001172 RNA-templated transcription
GO:0006351 DNA-templated transcription
GO:0039694 viral RNA genome replication

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Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4lq3, PDBe:4lq3, PDBj:4lq3
PDBsum4lq3
PubMed24316032
UniProtQ2N379

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