scPDB - 4gv8 entry

Protein Data Bank Entry:

PDB ID : 4gv8

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2012-08-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	DUTPase
ID:	Q8SDV3_BPPHA
AC:	Q8SDV3
Organism:	Staphylococcus phage phi11
Reign:	Viruses
TaxID:	12360
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	34 %
B	59 %
C	3 %
F	3 %

Ligand binding site composition:

B-Factor:	50.498
Number of residues:	35
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.044	556.875

% Hydrophobic	% Polar
36.97	63.03
According to VolSite

Ligand :

HET Code:	DUP
Formula:	C9H12N3O13P3
Molecular weight:	463.125 g/mol
DrugBank ID:	DB01965
Buried Surface Area:	67.37 %
Polar Surface area:	282.23 Å2

Number of
H-Bond Acceptors:	13
H-Bond Donors:	3
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
16.411	48.3693	-7.64279

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
O1B	CZ	ARG- 64	3.41	0	Ionic (Protein Cationic)	false
O2B	CZ	ARG- 64	3.85	0	Ionic (Protein Cationic)	false
O1B	NH2	ARG- 64	3.05	131.48	H-Bond (Protein Donor)	false
O1B	NE	ARG- 64	3	133.75	H-Bond (Protein Donor)	false
O2A	N	SER- 65	2.87	151.98	H-Bond (Protein Donor)	false
O2B	N	GLY- 66	2.99	141.45	H-Bond (Protein Donor)	false
C2'	CD1	ILE- 80	3.73	0	Hydrophobic	false
O3'	OD2	ASP- 81	2.74	153.24	H-Bond (Ligand Donor)	false
O3'	N	ASP- 81	2.96	166.99	H-Bond (Protein Donor)	false
C1'	CZ	TYR- 84	3.72	0	Hydrophobic	false
C2'	CD2	TYR- 84	3.54	0	Hydrophobic	false
C3'	CG	TYR- 84	4.06	0	Hydrophobic	false
C4'	CD1	TYR- 84	3.93	0	Hydrophobic	false
N3	O	GLY- 89	2.69	156.36	H-Bond (Ligand Donor)	false
O2	N	GLY- 89	2.93	166.32	H-Bond (Protein Donor)	false
O2A	NE2	GLN- 136	3.28	140.73	H-Bond (Protein Donor)	false
O4'	N	PHE- 164	3	160.19	H-Bond (Protein Donor)	false
C5'	CA	PHE- 164	4.37	0	Hydrophobic	false
O1A	MG	MG- 202	2	0	Metal Acceptor	false
O1B	MG	MG- 202	2.13	0	Metal Acceptor	false
O1G	MG	MG- 202	2.09	0	Metal Acceptor	false
O4	O	HOH- 308	2.78	160.55	H-Bond (Protein Donor)	false
O4	O	HOH- 310	2.83	179.99	H-Bond (Protein Donor)	false