scPDB - 2vp4 entry

Protein Data Bank Entry:

PDB ID : 2vp4

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2008-02-26

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Deoxynucleoside kinase
ID:	DNK_DROME
AC:	Q9XZT6
Organism:	Drosophila melanogaster
Reign:	Eukaryota
TaxID:	7227
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	27.973
Number of residues:	40
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.136	516.375

% Hydrophobic	% Polar
46.41	53.59
According to VolSite

Ligand :

HET Code:	DCP
Formula:	C9H12N3O13P3
Molecular weight:	463.125 g/mol
DrugBank ID:	DB03258
Buried Surface Area:	80.5 %
Polar Surface area:	288.71 Å2

Number of
H-Bond Acceptors:	15
H-Bond Donors:	2
Rings:	2
Aromatic rings:	0
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-0.176214	18.3134	10.727

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
C2'	CD1	ILE- 29	3.58	0	Hydrophobic	false
C3'	CG2	ILE- 29	3.92	0	Hydrophobic	false
O1B	N	GLY- 30	3.41	153.92	H-Bond (Protein Donor)	false
O2G	N	GLY- 32	2.95	123.5	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 33	2.73	169.01	H-Bond (Protein Donor)	false
O3B	NZ	LYS- 33	2.96	122.88	H-Bond (Protein Donor)	false
O2G	NZ	LYS- 33	2.83	166.91	H-Bond (Protein Donor)	false
O2G	N	LYS- 33	2.76	156.51	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 33	2.73	0	Ionic (Protein Cationic)	false
O2G	NZ	LYS- 33	2.83	0	Ionic (Protein Cationic)	false
O1G	N	THR- 34	2.9	171.45	H-Bond (Protein Donor)	false
C5'	CG2	VAL- 54	3.82	0	Hydrophobic	false
C1'	CZ3	TRP- 57	4.5	0	Hydrophobic	false
C5'	CZ3	TRP- 57	4.45	0	Hydrophobic	false
C1'	CD1	LEU- 66	3.89	0	Hydrophobic	false
C4'	CD1	LEU- 66	3.93	0	Hydrophobic	false
O3'	OH	TYR- 70	2.64	173.37	H-Bond (Protein Donor)	false
C1'	CZ	PHE- 80	4.2	0	Hydrophobic	false
N3	NE2	GLN- 81	2.77	170.75	H-Bond (Protein Donor)	false
O2	NE2	GLN- 81	3.42	121.8	H-Bond (Protein Donor)	false
N4	OE1	GLN- 81	3.19	147.17	H-Bond (Ligand Donor)	false
O1A	NE	ARG- 105	2.76	158.5	H-Bond (Protein Donor)	false
O2A	NE	ARG- 105	3.42	128.98	H-Bond (Protein Donor)	false
O2A	NH2	ARG- 105	2.76	146.79	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 105	3.76	0	Ionic (Protein Cationic)	false
O2A	CZ	ARG- 105	3.51	0	Ionic (Protein Cationic)	false
C2'	CE2	PHE- 114	3.85	0	Hydrophobic	false
O1B	NH2	ARG- 167	3.22	124.93	H-Bond (Protein Donor)	false
O1B	NH1	ARG- 167	3.22	124.81	H-Bond (Protein Donor)	false
O3G	NH1	ARG- 167	2.7	124.3	H-Bond (Protein Donor)	false
O1B	CZ	ARG- 167	3.57	0	Ionic (Protein Cationic)	false
O3G	CZ	ARG- 167	3.97	0	Ionic (Protein Cationic)	false
O2B	NH2	ARG- 169	2.67	158.27	H-Bond (Protein Donor)	false
O2B	NH1	ARG- 169	3.31	127.63	H-Bond (Protein Donor)	false
O2B	CZ	ARG- 169	3.41	0	Ionic (Protein Cationic)	false
O3'	OE2	GLU- 172	2.89	150.19	H-Bond (Ligand Donor)	false