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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:

3dnd

2.260 Å

X-ray

2008-07-02

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:cAMP-dependent protein kinase catalytic subunit alpha
ID:KAPCA_BOVIN
AC:P00517
Organism:Bos taurus
Reign:Eukaryota
TaxID:9913
EC Number:2.7.11.11


Chains:

Chain Name:Percentage of Residues
within binding site
A95 %
I5 %


Ligand binding site composition:

B-Factor:27.453
Number of residues:22
Including
Standard Amino Acids: 21
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.874756.000

% Hydrophobic% Polar
44.2055.80
According to VolSite

Ligand :
3dnd_1 Structure
HET Code: LL2
Formula: C10H10N2S
Molecular weight: 190.265 g/mol
DrugBank ID: DB08114
Buried Surface Area:70.37 %
Polar Surface area: 67.14 Å2
Number of
H-Bond Acceptors: 2
H-Bond Donors: 1
Rings: 2
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 2

Mass center Coordinates

XYZ
7.140319.857923.96892


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
C2CBLEU- 493.80Hydrophobic
C8CG2VAL- 574.130Hydrophobic
C2CG1VAL- 573.990Hydrophobic
S4CG1VAL- 573.790Hydrophobic
S4CBALA- 703.910Hydrophobic
N10OGLU- 1212.93135.57H-Bond
(Ligand Donor)
C12CGGLU- 1273.70Hydrophobic
S4CD1LEU- 1733.770Hydrophobic
C9CD2LEU- 1733.80Hydrophobic
C13CG2THR- 1833.430Hydrophobic
C2CE1PHE- 32740Hydrophobic