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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:

3ae4

2.910 Å

X-ray

2010-02-04

Molecular Function:
Binding Site :

Uniprot Annotation

Name:Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrialSuccinate dehydrogenase cytochrome b560 subunit, mitochondrial
ID:SDHB_PIGC560_PIG
AC:Q007T0D0VWV4
Organism:Sus scrofa
Reign:Eukaryota
TaxID:9823
EC Number:1.3.5.1/


Chains:

Chain Name:Percentage of Residues
within binding site
B41 %
C47 %
D12 %


Ligand binding site composition:

B-Factor:66.602
Number of residues:18
Including
Standard Amino Acids: 17
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.1862544.750

% Hydrophobic% Polar
63.7936.21
According to VolSite

Ligand :
3ae4_1 Structure
HET Code: N1M
Formula: C8H8INO
Molecular weight: 261.060 g/mol
DrugBank ID: -
Buried Surface Area:66.69 %
Polar Surface area: 29.1 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
12.7165-25.989560.7376


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
C4CBSER- 424.170Hydrophobic
C3CG1ILE- 434.150Hydrophobic
C5CGARG- 463.450Hydrophobic
OOHTYR- 912.65160.49H-Bond
(Protein Donor)
ONE1TRP- 1732.68142.97H-Bond
(Protein Donor)
C6CBHIS- 2164.140Hydrophobic
ICD1ILE- 2184.260Hydrophobic
C1CD1ILE- 2183.650Hydrophobic