Structure of PDB 3upf Chain A Binding Site BS01

Receptor Information
>3upf 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]
LPRPSGTYAGLPIADYGDAPPLSTKTMFWRTSPEKLPPGAWEPAYLGSKD
ERVDGPSLQQVMRDQLKPYSEPRGLLPPQEILDAVCDAIENRLENTLEPQ
KPWTFKKACESLDKNTSSGYPYHKQKSKDWTGSAFIGDLGDQATHANNMY
EMGKSMRPIYTAALKDELVKPDKIYGKIKKRLLWGSDLGTMIRAARAFGP
FCDALKETCIFNPIRVGMSMNEDGPFIFARHANFRYHMDADYTRWDSTQQ
RAILKRAGDIMVRLSPEPDLARVVMDDLLAPSLLDVGDYKIVVEEGLPSC
PCTTQLNSLAHWILTLCAMVEVTRVDPDIVMQESEFSFYGDDEVVSTNLE
LDMVKYTMALRRYGLLPTRADKEEPLERRQTLQGISFLRRAIVGDQFGWY
GRLDRASIDRQLLWTKGPNHQNPFETLPGHRPQLMALLGEAAMHGEKYYR
TVASRVSKEAAVVPRHRSVLRWVRFG
Ligand information
Ligand ID0BU
InChIInChI=1S/C35H26N4O21S6/c40-33(38-25-7-9-27(63(49,50)51)23-13-21(61(43,44)45)15-29(31(23)25)65(55,56)57)17-3-1-5-19(11-17)36-35(42)37-20-6-2-4-18(12-20)34(41)39-26-8-10-28(64(52,53)54)24-14-22(62(46,47)48)16-30(32(24)26)66(58,59)60/h1-16H,(H,38,40)(H,39,41)(H2,36,37,42)(H,43,44,45)(H,46,47,48)(H,49,50,51)(H,52,53,54)(H,55,56,57)(H,58,59,60)
InChIKeyJMONOAYAUIIKMS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.370O[S](=O)(=O)c1cc2c(ccc(NC(=O)c3cccc(NC(=O)Nc4cccc(c4)C(=O)Nc5ccc(c6cc(cc(c56)[S](O)(=O)=O)[S](O)(=O)=O)[S](O)(=O)=O)c3)c2c(c1)[S](O)(=O)=O)[S](O)(=O)=O
OpenEye OEToolkits 1.7.6c1cc(cc(c1)NC(=O)Nc2cccc(c2)C(=O)Nc3ccc(c4c3c(cc(c4)S(=O)(=O)O)S(=O)(=O)O)S(=O)(=O)O)C(=O)Nc5ccc(c6c5c(cc(c6)S(=O)(=O)O)S(=O)(=O)O)S(=O)(=O)O
ACDLabs 12.01O=S(=O)(O)c1c2c(cc(c1)S(=O)(=O)O)c(ccc2NC(=O)c3cc(ccc3)NC(=O)Nc4cccc(c4)C(=O)Nc5ccc(c6c5c(cc(c6)S(=O)(=O)O)S(=O)(=O)O)S(=O)(=O)O)S(=O)(=O)O
FormulaC35 H26 N4 O21 S6
Name8-({3-[({3-[(4,6,8-trisulfonaphthalen-1-yl)carbamoyl]phenyl}carbamoyl)amino]benzoyl}amino)naphthalene-1,3,5-trisulfonic acid;
NF023
ChEMBLCHEMBL1206126
DrugBank
ZINC
PDB chain3upf Chain A Residue 600 [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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PDB3upf Structure-Based Inhibition of Norovirus RNA-Dependent RNA Polymerases.
Resolution2.6 Å
Binding residue
(original residue number in PDB)		W42 D65 Q66 P69 E168 V170 K171 K174 K180 R182 R245 R392
Binding residue
(residue number reindexed from 1)		W41 D64 Q65 P68 E167 V169 K170 K173 K179 R181 R244 R389
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.70,IC50=200nM
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:3upf, PDBe:3upf, PDBj:3upf
PDBsum3upf
PubMed22446684
UniProtQ80J95|POLG_MNV1 Genome polyprotein (Gene Name=ORF1)

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