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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:

3ama

1.750 Å

X-ray

2010-08-18

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:cAMP-dependent protein kinase catalytic subunit alpha
ID:KAPCA_HUMAN
AC:P17612
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:2.7.11.11


Chains:

Chain Name:Percentage of Residues
within binding site
A97 %
B3 %


Ligand binding site composition:

B-Factor:24.389
Number of residues:37
Including
Standard Amino Acids: 34
Non Standard Amino Acids: 0
Water Molecules: 3
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.079955.125

% Hydrophobic% Polar
43.8256.18
According to VolSite

Ligand :
3ama_1 Structure
HET Code: SKE
Formula: C15H12F2N6O3S
Molecular weight: 394.356 g/mol
DrugBank ID: -
Buried Surface Area:67.8 %
Polar Surface area: 154.36 Å2
Number of
H-Bond Acceptors: 7
H-Bond Donors: 3
Rings: 3
Aromatic rings: 3
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 4

Mass center Coordinates

XYZ
-29.64649.815596.62241


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
C3CD1LEU- 494.180Hydrophobic
C5CBLEU- 494.040Hydrophobic
C7CD2LEU- 493.990Hydrophobic
F1CBLEU- 493.30Hydrophobic
C10CG1VAL- 574.350Hydrophobic
C12CBVAL- 574.40Hydrophobic
F1CG1VAL- 573.580Hydrophobic
F1CBALA- 704.340Hydrophobic
N1OGLU- 1212.79159.87H-Bond
(Ligand Donor)
N2NALA- 1233.04173.73H-Bond
(Protein Donor)
N3OALA- 1232.81151.8H-Bond
(Ligand Donor)
C14CGGLU- 1274.040Hydrophobic
F2CD2LEU- 1733.460Hydrophobic
N4OHOH- 4332.75150.68H-Bond
(Ligand Donor)