Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

3sfu

2.500 Å

X-ray

2011-06-14

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Polyprotein
ID:Q80J95_9CALI
AC:Q80J95
Organism:Murine norovirus 1
Reign:Viruses
TaxID:223997
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
C100 %


Ligand binding site composition:

B-Factor:26.610
Number of residues:22
Including
Standard Amino Acids: 22
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.236877.500

% Hydrophobic% Polar
34.2365.77
According to VolSite

Ligand :
3sfu_3 Structure
HET Code: RBV
Formula: C8H12N4O5
Molecular weight: 244.205 g/mol
DrugBank ID: DB00811
Buried Surface Area:52.76 %
Polar Surface area: 143.72 Å2
Number of
H-Bond Acceptors: 7
H-Bond Donors: 4
Rings: 2
Aromatic rings: 1
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 3

Mass center Coordinates

XYZ
-82.621547.3925-14.0416


Binding mode :
What is Poseview ?
  • 2D View
  • 3D View
Binding mode
BioSolveIT Image generated by PoseView
Protein
Binding Site
Ligand
Interaction pattern
hydrophobic (CA)
aromatic (CZ)
hydrogen bond acceptor (O)
hydrogen bond acceptor/donor (OG)
hydrogen bond donor (N)
positively ionized (NZ)
negatively ionized (OD1)
metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT
BioSolveIT


LigandProteinInteraction
AtomAtomResidueDistance
(Å)
Angle (°)Type
O2'OD1ASP- 2503.45140.03H-Bond
(Ligand Donor)
C2'CD2LEU- 3013.940Hydrophobic
C3'CBTHR- 3093.860Hydrophobic
C3'CBASN- 3124.020Hydrophobic
O5'OD1ASP- 3463.44133.57H-Bond
(Ligand Donor)