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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:

3vr8

2.810 Å

X-ray

2012-04-07

Molecular Function:
Binding Site :

Uniprot Annotation

Name:Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrialCytochrome b-large subunit
ID:O44074_ASCSUP92506_ASCSU
AC:O44074P92506
Organism:Ascaris suum
Reign:Eukaryota
TaxID:6253
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
B38 %
C54 %
D8 %


Ligand binding site composition:

B-Factor:89.090
Number of residues:24
Including
Standard Amino Acids: 23
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.4351998.000

% Hydrophobic% Polar
65.0334.97
According to VolSite

Ligand :
3vr8_1 Structure
HET Code: RQX
Formula: C15H22NO3
Molecular weight: 264.340 g/mol
DrugBank ID: -
Buried Surface Area:56.96 %
Polar Surface area: 71.01 Å2
Number of
H-Bond Acceptors: 3
H-Bond Donors: 1
Rings: 1
Aromatic rings: 0
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 5

Mass center Coordinates

XYZ
-30.6086-21.4875-47.5809


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
C9CD2LEU- 604.140Hydrophobic
C14CD2LEU- 603.720Hydrophobic
C1CE3TRP- 693.790Hydrophobic
NOGSER- 723.17167.75H-Bond
(Ligand Donor)
O3NH1ARG- 762.5169.82H-Bond
(Protein Donor)
O3NH2ARG- 763.22125.79H-Bond
(Protein Donor)
C15CE2TYR- 1073.210Hydrophobic
C9CBPRO- 1934.410Hydrophobic
C8CBSER- 1944.270Hydrophobic
C9CZ2TRP- 1973.990Hydrophobic
C8CBHIS- 2404.070Hydrophobic
C8CD1ILE- 2423.80Hydrophobic