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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:

3eon

2.550 Å

X-ray

2008-09-28

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Glutaryl-CoA dehydrogenase
ID:Q3JP94_BURP1
AC:Q3JP94
Organism:Burkholderia pseudomallei
Reign:Bacteria
TaxID:320372
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
C100 %


Ligand binding site composition:

B-Factor:35.545
Number of residues:21
Including
Standard Amino Acids: 21
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.594762.750

% Hydrophobic% Polar
67.7032.30
According to VolSite

Ligand :
3eon_1 Structure
HET Code: 341
Formula: C7H6F2O
Molecular weight: 144.119 g/mol
DrugBank ID: -
Buried Surface Area:51.27 %
Polar Surface area: 20.23 Å2
Number of
H-Bond Acceptors: 1
H-Bond Donors: 1
Rings: 1
Aromatic rings: 1
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 1

Mass center Coordinates

XYZ
-15.210871.36313.6592


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
O10NH2ARG- 973.03156.63H-Bond
(Protein Donor)
O10OGSER- 983.27158.82H-Bond
(Protein Donor)
F7CD2LEU- 2503.880Hydrophobic
C3CD1ILE- 2573.750Hydrophobic
C1CD1ILE- 2573.540Hydrophobic
C1CD1ILE- 2573.540Hydrophobic
F8CG1VAL- 3704.390Hydrophobic
F7CE2TYR- 3733.880Hydrophobic
C1CBTYR- 3733.810Hydrophobic
C2CGGLU- 3743.90Hydrophobic