Structure of PDB 5t6f Chain A Binding Site BS01

Receptor Information
>5t6f Chain A (length=165) Species: 524364 (Norovirus Hu/1968/US) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HAPPTLWSRVTKFGSGWGFWVSPTVFITTTHVVPTGVKEFFGEPLSSIAI
HQAGEFTQFRFSKKMRPDLTGMVLEEGCPEGTVCSVLIKRDSGELLPLAV
RMGAIASMRIQGRLVHGQSGMLLLGTIPGDCGAPYVHKRGNDWVVCGVHA
AATKSGNTVVCAVQA
Ligand information
Ligand IDN38
InChIInChI=1S/C26H41N3O7S/c1-35-22-8-10-23(11-9-22)36-14-5-15-37(33,34)29-24(16-19-6-3-2-4-7-19)26(32)28-21(18-30)17-20-12-13-27-25(20)31/h8-11,19-21,24,29-30H,2-7,12-18H2,1H3,(H,27,31)(H,28,32)/t20-,21-,24-/m0/s1
InChIKeyJSFDYEDTWWEPLF-HFMPRLQTSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6COc1ccc(cc1)OCCCS(=O)(=O)N[C@@H](CC2CCCCC2)C(=O)N[C@@H](C[C@@H]3CCNC3=O)CO
CACTVS 3.385COc1ccc(OCCC[S](=O)(=O)N[CH](CC2CCCCC2)C(=O)N[CH](CO)C[CH]3CCNC3=O)cc1
CACTVS 3.385COc1ccc(OCCC[S](=O)(=O)N[C@@H](CC2CCCCC2)C(=O)N[C@H](CO)C[C@@H]3CCNC3=O)cc1
ACDLabs 12.01COc3ccc(OCCCS(NC(CC1CCCCC1)C(NC(CO)CC2CCNC2=O)=O)(=O)=O)cc3
OpenEye OEToolkits 2.0.6COc1ccc(cc1)OCCCS(=O)(=O)NC(CC2CCCCC2)C(=O)NC(CC3CCNC3=O)CO
FormulaC26 H41 N3 O7 S
Name3-cyclohexyl-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-N~2~-{[3-(4-methoxyphenoxy)propyl]sulfonyl}-L- alaninamide;
3-cyclohexyl-N~2~-{[3-(4-methoxyphenoxy)propyl]sulfonyl}-N-{(2S)-1-oxo-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-alan inamide (bound form)
ChEMBL
DrugBank
ZINCZINC000584905779
PDB chain5t6f Chain A Residue 201 [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]
PDB5t6f Structure-based exploration and exploitation of the S4 subsite of norovirus 3CL protease in the design of potent and permeable inhibitors.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		E54 I109 Q110 R112 T134 I135 P136 C139 H157 A158 A159 A160 T161 V168
Binding residue
(residue number reindexed from 1)		E55 I110 Q111 R113 T126 I127 P128 C131 H149 A150 A151 A152 T153 V160
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.80,IC50=1.6uM
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:0004197 cysteine-type endopeptidase activity
Biological Process
GO:0006508 proteolysis

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5t6f, PDBe:5t6f, PDBj:5t6f
PDBsum5t6f
PubMed27914364
UniProtQ83883|POLG_NVN68 Genome polyprotein (Gene Name=ORF1)

[Back to BioLiP]