scPDB - 4dgm entry

Protein Data Bank Entry:

PDB ID : 4dgm

Resolution :1.650 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:	28.961
Number of residues:	27
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.910	1049.625

% Hydrophobic	% Polar
48.87	51.13
According to VolSite

Ligand :

HET Code:	AGI
Formula:	C15H9O5
Molecular weight:	269.229 g/mol
DrugBank ID:	DB07352
Buried Surface Area:	68.65 %
Polar Surface area:	89.82 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	2
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
21.9016	7.68865	19.2748

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
CAN	CG2	VAL- 45	3.72	0	Hydrophobic	false
CAH	CG2	VAL- 53	4.06	0	Hydrophobic	false
CAP	CG1	VAL- 53	4.39	0	Hydrophobic	false
CAK	CG1	VAL- 53	4.19	0	Hydrophobic	false
CAP	CG2	ILE- 66	4.09	0	Hydrophobic	false
CAT	CD1	ILE- 66	3.74	0	Hydrophobic	false
OAB	NZ	LYS- 68	3	176.6	H-Bond (Protein Donor)	false
CAF	CD	LYS- 68	3.77	0	Hydrophobic	false
CAG	CG2	VAL- 95	3.89	0	Hydrophobic	false
CAG	CB	PHE- 113	4.35	0	Hydrophobic	false
OAA	N	VAL- 116	3.19	152.56	H-Bond (Protein Donor)	false
OAD	O	VAL- 116	2.66	122.83	H-Bond (Ligand Donor)	false
CAO	CB	ASN- 118	3.86	0	Hydrophobic	false
CAT	SD	MET- 163	3.41	0	Hydrophobic	false
CAG	CG2	ILE- 174	3.61	0	Hydrophobic	false
CAE	CB	ILE- 174	3.72	0	Hydrophobic	false
CAH	CD1	ILE- 174	3.43	0	Hydrophobic	false
OAB	N	ASP- 175	3.11	130.96	H-Bond (Protein Donor)	false
CAF	CB	ASP- 175	4.14	0	Hydrophobic	false