scPDB - 4kbk entry

Protein Data Bank Entry:

PDB ID : 4kbk

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2013-04-23

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

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
B	100 %

Ligand binding site composition:

B-Factor:	38.718
Number of residues:	33
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.060	668.250

% Hydrophobic	% Polar
52.02	47.98
According to VolSite

Ligand :

HET Code:	1QG
Formula:	C19H20FN4O
Molecular weight:	339.387 g/mol
DrugBank ID:	-
Buried Surface Area:	59.42 %
Polar Surface area:	56.55 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	1
Rings:	4
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	3

Mass center Coordinates

X	Y	Z
-6.35776	-1.98332	11.5858

Binding mode :

What is Poseview ?

2D View
3D View

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

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
C7	CD1	ILE- 23	4.33	0	Hydrophobic	false
C6	CG2	ILE- 23	3.63	0	Hydrophobic	false
C1	CG1	ILE- 23	4.3	0	Hydrophobic	false
C5	CD1	ILE- 23	3.55	0	Hydrophobic	false
C11	CG2	ILE- 23	4.38	0	Hydrophobic	false
C6	CB	ALA- 36	3.73	0	Hydrophobic	false
C12	CB	ALA- 36	3.8	0	Hydrophobic	false
C9	CD	LYS- 38	3.87	0	Hydrophobic	false
F1	CB	LYS- 38	3.43	0	Hydrophobic	false
F1	CE	MET- 80	3.39	0	Hydrophobic	false
C12	SD	MET- 82	3.61	0	Hydrophobic	false
C5	SD	MET- 82	4.2	0	Hydrophobic	false
C9	CE	MET- 82	3.45	0	Hydrophobic	false
F1	CB	MET- 82	3.62	0	Hydrophobic	false
N3	N	LEU- 85	2.99	160.25	H-Bond (Protein Donor)	false
C12	CD1	LEU- 85	4.48	0	Hydrophobic	false
C17	CD2	LEU- 135	3.9	0	Hydrophobic	false
C11	CD2	LEU- 135	3.72	0	Hydrophobic	false
C1	CD1	ILE- 148	3.65	0	Hydrophobic	false