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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:

4dg3

1.800 Å

X-ray

2012-01-24

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:cAMP-dependent protein kinase catalytic subunit alpha
ID:KAPCA_MOUSE
AC:P05132
Organism:Mus musculus
Reign:Eukaryota
TaxID:10090
EC Number:2.7.11.11


Chains:

Chain Name:Percentage of Residues
within binding site
E89 %
A11 %


Ligand binding site composition:

B-Factor:24.356
Number of residues:50
Including
Standard Amino Acids: 44
Non Standard Amino Acids: 2
Water Molecules: 4
Cofactors:
Metals: MG MG

Cavity properties

LigandabilityVolume (Å3)
0.063428.625

% Hydrophobic% Polar
51.1848.82
According to VolSite

Ligand :
4dg3_1 Structure
HET Code: ANP
Formula: C10H13N6O12P3
Molecular weight: 502.164 g/mol
DrugBank ID: -
Buried Surface Area:76.69 %
Polar Surface area: 322.68 Å2
Number of
H-Bond Acceptors: 16
H-Bond Donors: 4
Rings: 3
Aromatic rings: 2
Anionic atoms: 4
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 8

Mass center Coordinates

XYZ
-26.06849.51311.91194


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
O3'NH2ARG- 182.95142.33H-Bond
(Protein Donor)
O1GNALA- 212.99176.29H-Bond
(Protein Donor)
C1'CG1VAL- 574.250Hydrophobic
C5'CG2VAL- 573.660Hydrophobic
O1BNZLYS- 722.88131.89H-Bond
(Protein Donor)
O1ANZLYS- 722.86165.39H-Bond
(Protein Donor)
O1BNZLYS- 722.880Ionic
(Protein Cationic)
O1ANZLYS- 722.860Ionic
(Protein Cationic)
N6OGLU- 1212.87160.58H-Bond
(Ligand Donor)
N1NVAL- 1233.08171.52H-Bond
(Protein Donor)
C2'CGGLU- 1273.980Hydrophobic
O2'OE2GLU- 1272.58147.8H-Bond
(Ligand Donor)
O1GNZLYS- 1683.890Ionic
(Protein Cationic)
O2GNZLYS- 1682.60Ionic
(Protein Cationic)
O2GNZLYS- 1682.6151.53H-Bond
(Protein Donor)
O3'OGLU- 1702.71160.17H-Bond
(Ligand Donor)
C2'CD2LEU- 1733.970Hydrophobic
N7OG1THR- 1832.93175.28H-Bond
(Protein Donor)
C1'CE1PHE- 3274.430Hydrophobic
O2GMG MG- 4022.10Metal Acceptor
O2AMG MG- 4021.990Metal Acceptor
O3GMG MG- 4031.980Metal Acceptor
O1BMG MG- 4032.050Metal Acceptor
O1AOHOH- 5282.79179.98H-Bond
(Protein Donor)
O2'OHOH- 6853.11148.37H-Bond
(Protein Donor)