scPDB - 2oke entry

Protein Data Bank Entry:

PDB ID : 2oke

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2007-01-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	DUTP pyrophosphatase
ID:	A4GD96_9POXV
AC:	A4GD96
Organism:	Vaccinia virus
Reign:	Viruses
TaxID:	10245
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
B	37 %
C	63 %

Ligand binding site composition:

B-Factor:	17.300
Number of residues:	29
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.186	249.750

% Hydrophobic	% Polar
41.89	58.11
According to VolSite

Ligand :

HET Code:	DUP
Formula:	C9H12N3O13P3
Molecular weight:	463.125 g/mol
DrugBank ID:	DB01965
Buried Surface Area:	61.43 %
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
-14.45	-49.0903	-10.5524

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
C5'	CB	SER- 70	4.32	0	Hydrophobic	false
O2G	OG	SER- 70	2.68	146.66	H-Bond (Protein Donor)	false
O2G	N	SER- 70	2.75	149.14	H-Bond (Protein Donor)	false
O1B	N	GLY- 71	2.89	145.13	H-Bond (Protein Donor)	false
O4	N	GLY- 82	3.09	126.88	H-Bond (Protein Donor)	false
C2'	CD1	ILE- 84	4.42	0	Hydrophobic	false
O3'	OD1	ASP- 85	2.63	151.16	H-Bond (Ligand Donor)	false
C1'	CZ	TYR- 88	3.79	0	Hydrophobic	false
C4'	CE1	TYR- 88	3.96	0	Hydrophobic	false
C2'	CD1	TYR- 88	3.72	0	Hydrophobic	false
N3	O	GLY- 93	2.73	158.4	H-Bond (Ligand Donor)	false
O2	N	GLY- 93	3.12	170.3	H-Bond (Protein Donor)	false
O4	O	HOH- 302	2.72	179.95	H-Bond (Protein Donor)	false