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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:

5c3j

2.800 Å

X-ray

2015-06-17

Molecular Function:
Binding Site :

Uniprot Annotation

Name:Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrialSuccinate dehydrogenase cytochrome b560
ID:O44074_ASCSUF1LC27_ASCSU
AC:O44074F1LC27
Organism:Ascaris suum
Reign:Eukaryota
TaxID:6253
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
F35 %
G52 %
H13 %


Ligand binding site composition:

B-Factor:54.312
Number of residues:23
Including
Standard Amino Acids: 22
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.8731687.500

% Hydrophobic% Polar
58.2041.80
According to VolSite

Ligand :
5c3j_2 Structure
HET Code: UQ1
Formula: C14H18O4
Molecular weight: 250.290 g/mol
DrugBank ID: DB08689
Buried Surface Area:52.03 %
Polar Surface area: 52.6 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 0
Rings: 1
Aromatic rings: 0
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 4

Mass center Coordinates

XYZ
60.6892-47.181789.9752


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
C7CD2LEU- 603.80Hydrophobic
CM5CZ3TRP- 693.450Hydrophobic
O3OGSER- 723.37151.19H-Bond
(Protein Donor)
CM3CBSER- 724.240Hydrophobic
CM3CDARG- 763.790Hydrophobic
O1OHTYR- 1072.6140.57H-Bond
(Protein Donor)
C11CE2TYR- 1073.650Hydrophobic
CM2CBPRO- 1934.110Hydrophobic
C7CZ2TRP- 1973.540Hydrophobic
C11CZ2TRP- 1973.940Hydrophobic
CM2CD1ILE- 2423.980Hydrophobic