scPDB - 4dgn entry

Protein Data Bank Entry:

PDB ID : 4dgn

Resolution :1.750 Å

Experimental Method : X-ray

Deposition Date : 2012-01-26

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Casein kinase II subunit alpha
ID:	CSK2A_MAIZE
AC:	P28523
Organism:	Zea mays
Reign:	Eukaryota
TaxID:	4577
EC Number:	2.7.11.1

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	33.447
Number of residues:	28
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.893	904.500

% Hydrophobic	% Polar
44.03	55.97
According to VolSite

Ligand :

HET Code:	LU2
Formula:	C15H9O6
Molecular weight:	285.228 g/mol
DrugBank ID:	-
Buried Surface Area:	69.18 %
Polar Surface area:	110.05 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	1

Mass center Coordinates

X	Y	Z
22.0198	7.64362	19.0455

Binding mode :

What is Poseview ?

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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
C2	CG2	VAL- 45	3.62	0	Hydrophobic	false
C1	CG1	VAL- 53	4.26	0	Hydrophobic	false
C11	CG1	VAL- 53	4.23	0	Hydrophobic	false
C5	CD1	ILE- 66	3.78	0	Hydrophobic	false
C10	CG2	ILE- 66	4.14	0	Hydrophobic	false
O5	NZ	LYS- 68	3.31	132.01	H-Bond (Protein Donor)	false
O6	NZ	LYS- 68	2.95	145.98	H-Bond (Protein Donor)	false
C13	CD	LYS- 68	3.85	0	Hydrophobic	false
C15	CG2	VAL- 95	3.87	0	Hydrophobic	false
C15	CB	PHE- 113	4.38	0	Hydrophobic	false
C14	CE2	PHE- 113	3.48	0	Hydrophobic	false
O2	O	VAL- 116	2.65	120.58	H-Bond (Ligand Donor)	false
O3	N	VAL- 116	3.17	143.65	H-Bond (Protein Donor)	false
C4	CB	ASN- 118	3.86	0	Hydrophobic	false
C5	SD	MET- 163	3.44	0	Hydrophobic	false
C15	CG2	ILE- 174	3.65	0	Hydrophobic	false
C11	CD1	ILE- 174	3.32	0	Hydrophobic	false
C14	CB	ILE- 174	3.8	0	Hydrophobic	false
O6	N	ASP- 175	3.11	131	H-Bond (Protein Donor)	false
C12	CB	ASP- 175	4.12	0	Hydrophobic	false
O6	O	HOH- 508	2.59	162.37	H-Bond (Protein Donor)	false