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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:

4hgt

1.800 Å

X-ray

2012-10-08

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Casein kinase I isoform delta
ID:KC1D_HUMAN
AC:P48730
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:2.7.11.1


Chains:

Chain Name:Percentage of Residues
within binding site
A22 %
B78 %


Ligand binding site composition:

B-Factor:24.342
Number of residues:37
Including
Standard Amino Acids: 36
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.109614.250

% Hydrophobic% Polar
59.8940.11
According to VolSite

Ligand :
4hgt_2 Structure
HET Code: 15G
Formula: C20H17F2N3O3
Molecular weight: 385.364 g/mol
DrugBank ID: -
Buried Surface Area:65.4 %
Polar Surface area: 76.24 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 2
Rings: 4
Aromatic rings: 3
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 5

Mass center Coordinates

XYZ
0.7293574.06746-3.53457


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
C16CD1ILE- 153.630Hydrophobic
F2CG2ILE- 153.840Hydrophobic
C12CD1ILE- 233.850Hydrophobic
C20CD2LEU- 254.180Hydrophobic
C4CD1LEU- 254.230Hydrophobic
F1CG2THR- 273.360Hydrophobic
C17CBALA- 363.820Hydrophobic
O1NZLYS- 382.84157.37H-Bond
(Protein Donor)
C7CGPRO- 663.630Hydrophobic
C7CBMET- 823.660Hydrophobic
C17CEMET- 824.170Hydrophobic
C20CD1LEU- 843.590Hydrophobic
C7CD1LEU- 854.190Hydrophobic
N1NLEU- 852.81156.35H-Bond
(Protein Donor)
C20CD2LEU- 1354.170Hydrophobic
C16CD2LEU- 1353.660Hydrophobic
C7CG2ILE- 1483.980Hydrophobic
C12CD1ILE- 1484.40Hydrophobic
C15CD1ILE- 1484.310Hydrophobic