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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:

5f0a

2.600 Å

X-ray

2015-11-27

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:cGMP-dependent protein kinase, putative
ID:A5K0N4_PLAVS
AC:A5K0N4
Organism:Plasmodium vivax
Reign:Eukaryota
TaxID:126793
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:79.234
Number of residues:30
Including
Standard Amino Acids: 30
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.978506.250

% Hydrophobic% Polar
56.6743.33
According to VolSite

Ligand :
5f0a_1 Structure
HET Code: 1FB
Formula: C15H16ClN5O
Molecular weight: 317.773 g/mol
DrugBank ID: -
Buried Surface Area:65.55 %
Polar Surface area: 78.85 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 1
Rings: 3
Aromatic rings: 3
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 3

Mass center Coordinates

XYZ
-25.669169.774830.4342


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
CAACBVAL- 5483.980Hydrophobic
CAHCG1VAL- 5483.990Hydrophobic
C5CBALA- 5614.390Hydrophobic
CAHCBALA- 5613.760Hydrophobic
CL1CDLYS- 5634.130Hydrophobic
CAGCBLYS- 5633.390Hydrophobic
CL1CG2THR- 5864.120Hydrophobic
CL1CBPHE- 6093.50Hydrophobic
CAOCG2THR- 6113.450Hydrophobic
CAGCG2THR- 6113.360Hydrophobic
NADOGLU- 6122.85149.36H-Bond
(Ligand Donor)
N1NVAL- 6143.08167.09H-Bond
(Protein Donor)
CABCD2LEU- 6644.30Hydrophobic
CACCD2LEU- 6644.440Hydrophobic
C5CD1LEU- 6643.440Hydrophobic
CACCD1ILE- 6743.830Hydrophobic