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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:

2fbw

2.100 Å

X-ray

2005-12-10

Molecular Function:
Binding Site :

Uniprot Annotation

Name:Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrialSuccinate dehydrogenase cytochrome b, large subunit
ID:SDHB_CHICKD0VWW3_CHICK
AC:Q9YHT2D0VWW3
Organism:Gallus gallus
Reign:Eukaryota
TaxID:9031
EC Number:1.3.5.1/


Chains:

Chain Name:Percentage of Residues
within binding site
O40 %
P50 %
Q10 %


Ligand binding site composition:

B-Factor:29.271
Number of residues:21
Including
Standard Amino Acids: 19
Non Standard Amino Acids: 1
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.213263.250

% Hydrophobic% Polar
50.0050.00
According to VolSite

Ligand :
2fbw_2 Structure
HET Code: CBE
Formula: C12H13NO2S
Molecular weight: 235.302 g/mol
DrugBank ID: DB04657
Buried Surface Area:63.48 %
Polar Surface area: 63.63 Å2
Number of
H-Bond Acceptors: 3
H-Bond Donors: 1
Rings: 2
Aromatic rings: 1
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 2

Mass center Coordinates

XYZ
44.9265-16.01815.44988


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
C14CG1ILE- 273.610Hydrophobic
C15CD1ILE- 273.770Hydrophobic
C13CEMET- 363.560Hydrophobic
C16CG2ILE- 404.420Hydrophobic
C12CG2ILE- 403.890Hydrophobic
C6CDARG- 434.470Hydrophobic
S4CZTYR- 584.470Hydrophobic
O9OHTYR- 582.68176.82H-Bond
(Protein Donor)
C12CGPRO- 1693.790Hydrophobic
O9NE1TRP- 1732.87151.8H-Bond
(Protein Donor)
C6CBHIS- 2163.50Hydrophobic
C5CD1ILE- 2183.70Hydrophobic
N10OHOH- 16873.09153H-Bond
(Ligand Donor)