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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Protein Data Bank Entry:

3vws

2.100 Å

X-ray

2012-08-31

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Genome polyprotein
ID:Q6DLV0_9FLAV
AC:Q6DLV0
Organism:Dengue virus 3
Reign:Viruses
TaxID:11069
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:58.988
Number of residues:24
Including
Standard Amino Acids: 22
Non Standard Amino Acids: 1
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.942968.625

% Hydrophobic% Polar
39.7260.28
According to VolSite

Ligand :
3vws_1 Structure
HET Code: VWS
Formula: C16H10ClNO5S
Molecular weight: 363.772 g/mol
DrugBank ID: -
Buried Surface Area:46.63 %
Polar Surface area: 109.89 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 0
Rings: 3
Aromatic rings: 3
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 4

Mass center Coordinates

XYZ
32.008964.740815.2442


Binding mode :
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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
CL1CE1PHE- 3984.210Hydrophobic
O1ND2ASN- 4052.66138.3H-Bond
(Protein Donor)
C3CG1VAL- 4113.970Hydrophobic
C4CZPHE- 4123.350Hydrophobic
O4NTHR- 4132.88156.75H-Bond
(Protein Donor)
O5OG1THR- 4132.85166.01H-Bond
(Protein Donor)
CL1CD1PHE- 4853.350Hydrophobic
CL1CG2VAL- 6034.270Hydrophobic