scPDB - 1pr6 entry

Protein Data Bank Entry:

PDB ID : 1pr6

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2003-06-19

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_ECO57
AC:	P0ABP9
Organism:	Escherichia coli O157:H7
Reign:	Bacteria
TaxID:	83334
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	20.918
Number of residues:	25
Including
Standard Amino Acids:	25
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.722	648.000

% Hydrophobic	% Polar
50.52	49.48
According to VolSite

Ligand :

HET Code:	XYA
Formula:	C10H13N5O4
Molecular weight:	267.241 g/mol
DrugBank ID:	DB03528
Buried Surface Area:	63.35 %
Polar Surface area:	139.54 Å2

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

Mass center Coordinates

X	Y	Z
51.5318	51.0975	28.1754

Binding mode :

What is Poseview ?

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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'	CG	MET- 64	4.42	0	Hydrophobic	false
C5'	SD	MET- 64	3.67	0	Hydrophobic	false
C5'	CD2	PHE- 159	4	0	Hydrophobic	false
C2'	CB	GLU- 179	4.3	0	Hydrophobic	false
C5'	SD	MET- 180	4.15	0	Hydrophobic	false
C2'	CG	MET- 180	4.07	0	Hydrophobic	false
O2'	N	MET- 180	2.96	130.29	H-Bond (Protein Donor)	false
O2'	OE1	GLU- 181	2.77	141.25	H-Bond (Ligand Donor)	false
O3'	OE2	GLU- 181	2.82	157.81	H-Bond (Ligand Donor)	false
N6	OD2	ASP- 204	3.01	153.56	H-Bond (Ligand Donor)	false