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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:

3uku

2.750 Å

X-ray

2011-11-09

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Actin-related protein 3
ID:ARP3_BOVIN
AC:P61157
Organism:Bos taurus
Reign:Eukaryota
TaxID:9913
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:56.827
Number of residues:33
Including
Standard Amino Acids: 32
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.1551431.000

% Hydrophobic% Polar
44.1055.90
According to VolSite

Ligand :
3uku_1 Structure
HET Code: C69
Formula: C17H16BrNO3S
Molecular weight: 394.283 g/mol
DrugBank ID: -
Buried Surface Area:68.86 %
Polar Surface area: 64.07 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 0
Rings: 3
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 4

Mass center Coordinates

XYZ
12.847218.115252.6169


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
CAUSGCYS- 123.960Hydrophobic
CALCGGLU- 844.240Hydrophobic
CAOCBGLU- 843.670Hydrophobic
BRACZ3TRP- 864.320Hydrophobic
CAPCH2TRP- 863.460Hydrophobic
CANSDMET- 893.910Hydrophobic
CACCEMET- 893.80Hydrophobic
CAJCGMET- 894.170Hydrophobic
CAUCEMET- 893.940Hydrophobic
CAVCGMET- 933.90Hydrophobic
SASCBLEU- 1124.370Hydrophobic
CATCBLEU- 1124.190Hydrophobic
CAVCD1LEU- 1124.120Hydrophobic
SASCBGLU- 1143.730Hydrophobic
CABCGPRO- 1154.370Hydrophobic
OAWND2ASN- 1182.95143.96H-Bond
(Protein Donor)
CARCBTHR- 1263.610Hydrophobic
SASCG2THR- 1264.280Hydrophobic
CAICG2THR- 1263.660Hydrophobic
BRACD1ILE- 1293.730Hydrophobic
CARCD1ILE- 1414.210Hydrophobic
SASCG2ILE- 1414.030Hydrophobic