scPDB - 2vp2 entry

Protein Data Bank Entry:

PDB ID : 2vp2

Resolution :2.500 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
A	100 %

Ligand binding site composition:

B-Factor:	26.870
Number of residues:	45
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.027	499.500

% Hydrophobic	% Polar
49.32	50.68
According to VolSite

Ligand :

HET Code:	DGT
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB02181
Buried Surface Area:	80.69 %
Polar Surface area:	315.33 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	3
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
-2.65313	18.9845	10.3172

Binding mode :

What is Poseview ?

2D View
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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
C3'	CG1	ILE- 29	3.86	0	Hydrophobic	false
C2'	CD1	ILE- 29	3.54	0	Hydrophobic	false
O2B	N	GLY- 30	3.49	168.39	H-Bond (Protein Donor)	false
O3G	N	GLY- 32	2.88	126.9	H-Bond (Protein Donor)	false
O3G	N	LYS- 33	2.64	152.46	H-Bond (Protein Donor)	false
O3G	NZ	LYS- 33	2.75	161.88	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 33	2.71	176.19	H-Bond (Protein Donor)	false
O3G	NZ	LYS- 33	2.75	0	Ionic (Protein Cationic)	false
O1A	NZ	LYS- 33	2.71	0	Ionic (Protein Cationic)	false
O1G	N	THR- 34	3.09	168.16	H-Bond (Protein Donor)	false
C5'	CG1	VAL- 54	3.41	0	Hydrophobic	false
C5'	CZ3	TRP- 57	4.31	0	Hydrophobic	false
C4'	CD1	LEU- 66	4.04	0	Hydrophobic	false
C1'	CD1	LEU- 66	3.82	0	Hydrophobic	false
O3'	OH	TYR- 70	2.75	175.63	H-Bond (Protein Donor)	false
C1'	CZ	PHE- 80	4.37	0	Hydrophobic	false
N7	NE2	GLN- 81	3.3	129.32	H-Bond (Protein Donor)	false
O6	NE2	GLN- 81	2.7	144.63	H-Bond (Protein Donor)	false
O1A	NH2	ARG- 105	2.9	149.3	H-Bond (Protein Donor)	false
O2A	NE	ARG- 105	2.92	175.12	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 105	3.73	0	Ionic (Protein Cationic)	false
O2A	CZ	ARG- 105	3.73	0	Ionic (Protein Cationic)	false
DuAr	DuAr	PHE- 114	3.8	0	Aromatic Face/Face	false
C2'	CE2	PHE- 114	3.75	0	Hydrophobic	false
O2G	NH1	ARG- 167	2.66	128.76	H-Bond (Protein Donor)	false
O2B	NH1	ARG- 167	3.12	121.41	H-Bond (Protein Donor)	false
O2B	NH2	ARG- 167	3.13	121.13	H-Bond (Protein Donor)	false
O2G	CZ	ARG- 167	3.9	0	Ionic (Protein Cationic)	false
O2B	CZ	ARG- 167	3.45	0	Ionic (Protein Cationic)	false
O1B	NH2	ARG- 169	2.87	178.84	H-Bond (Protein Donor)	false
O2B	NH1	ARG- 169	3.17	155.99	H-Bond (Protein Donor)	false
O1B	CZ	ARG- 169	3.7	0	Ionic (Protein Cationic)	false
O3'	OE2	GLU- 172	2.89	157.49	H-Bond (Ligand Donor)	false