scPDB - 1day entry

Protein Data Bank Entry:

PDB ID : 1day

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 1999-11-01

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:	35.792
Number of residues:	40
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	2
Water Molecules:	1
Cofactors:
Metals:	MG MG

Cavity properties

Ligandability	Volume (Å3)
0.628	823.500

% Hydrophobic	% Polar
45.08	54.92
According to VolSite

Ligand :

HET Code:	GNP
Formula:	C10H13N6O13P3
Molecular weight:	518.164 g/mol
DrugBank ID:	DB02082
Buried Surface Area:	64.44 %
Polar Surface area:	338.36 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	5
Rings:	3
Aromatic rings:	1
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
23.3468	4.60062	19.3206

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
C1'	CG2	VAL- 45	3.82	0	Hydrophobic	false
O1B	OG	SER- 51	2.52	164.89	H-Bond (Protein Donor)	false
C5'	CG2	VAL- 53	3.89	0	Hydrophobic	false
O1B	NZ	LYS- 68	3.93	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 68	2.63	0	Ionic (Protein Cationic)	false
O1A	NZ	LYS- 68	3.42	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 68	2.63	137.06	H-Bond (Protein Donor)	false
O6	N	VAL- 116	3.15	149.17	H-Bond (Protein Donor)	false
N1	O	VAL- 116	2.8	148.79	H-Bond (Ligand Donor)	false
N2	O	VAL- 116	3.2	137.38	H-Bond (Ligand Donor)	false
O1G	NZ	LYS- 158	2.96	156.19	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 158	2.96	0	Ionic (Protein Cationic)	false
O2G	NZ	LYS- 158	3.7	0	Ionic (Protein Cationic)	false
O3'	O	HIS- 160	2.54	162.24	H-Bond (Ligand Donor)	false
C2'	CE	MET- 163	3.74	0	Hydrophobic	false
C3'	CD1	ILE- 174	4.01	0	Hydrophobic	false
O3G	MG	MG- 341	2.1	0	Metal Acceptor	false
O2B	MG	MG- 341	2.29	0	Metal Acceptor	false
O1G	MG	MG- 342	1.84	0	Metal Acceptor	false
O3A	MG	MG- 342	2.77	0	Metal Acceptor	false
O2A	MG	MG- 342	1.87	0	Metal Acceptor	false