scPDB - 2zi6 entry

Protein Data Bank Entry:

PDB ID : 2zi6

Resolution :1.770 Å

Experimental Method : X-ray

Deposition Date : 2008-02-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Deoxycytidine kinase
ID:	DCK_HUMAN
AC:	P27707
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.7.1.74

Chains:

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

Ligand binding site composition:

B-Factor:	26.443
Number of residues:	29
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.689	887.625

% Hydrophobic	% Polar
47.91	52.09
According to VolSite

Ligand :

HET Code:	3D1
Formula:	C10H13N5O3
Molecular weight:	251.242 g/mol
DrugBank ID:	-
Buried Surface Area:	64.46 %
Polar Surface area:	119.31 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	2

Mass center Coordinates

X	Y	Z
82.4686	8.14944	20.8646

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'	CD1	ILE- 3030	3.72	0	Hydrophobic	false
C5'	CG1	VAL- 3055	3.62	0	Hydrophobic	false
C4'	CD1	LEU- 3082	4.37	0	Hydrophobic	false
O3'	OH	TYR- 3086	3.11	167.24	H-Bond (Ligand Donor)	false
N6	OE1	GLN- 3097	3.43	147.8	H-Bond (Ligand Donor)	false
N7	NE2	GLN- 3097	2.87	164.55	H-Bond (Protein Donor)	false
N6	OD1	ASP- 3133	2.66	177.81	H-Bond (Ligand Donor)	false
DuAr	DuAr	PHE- 3137	3.8	0	Aromatic Face/Face	false
C2'	CE2	PHE- 3137	3.35	0	Hydrophobic	false