scPDB - 4da0 entry

Protein Data Bank Entry:

PDB ID : 4da0

Resolution :2.950 Å

Experimental Method : X-ray

Deposition Date : 2012-01-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Purine nucleoside phosphorylase DeoD-type
ID:	DEOD_BACSU
AC:	O34925
Organism:	Bacillus subtilis
Reign:	Bacteria
TaxID:	224308
EC Number:	2.4.2.1

Chains:

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

Ligand binding site composition:

B-Factor:	58.467
Number of residues:	27
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	CL

Cavity properties

Ligandability	Volume (Å3)
0.829	580.500

% Hydrophobic	% Polar
50.58	49.42
According to VolSite

Ligand :

HET Code:	GNG
Formula:	C10H13N5O4
Molecular weight:	267.241 g/mol
DrugBank ID:	-
Buried Surface Area:	59.95 %
Polar Surface area:	134.99 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	2

Mass center Coordinates

X	Y	Z
-7.15326	-54.2366	-23.5374

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'	SD	MET- 64	3.99	0	Hydrophobic	false
C5'	CE1	PHE- 159	3.6	0	Hydrophobic	false
C2'	CB	GLU- 178	3.7	0	Hydrophobic	false
C2'	CG	MET- 179	3.91	0	Hydrophobic	false
C3'	SD	MET- 179	3.65	0	Hydrophobic	false
O3'	OE1	GLU- 180	2.64	136.16	H-Bond (Ligand Donor)	false
O3'	OE2	GLU- 180	2.61	134.65	H-Bond (Ligand Donor)	false
N7	OG	SER- 202	2.69	156.61	H-Bond (Protein Donor)	false