scPDB - 1pk9 entry

Protein Data Bank Entry:

PDB ID : 1pk9

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2003-06-05

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
B	100 %

Ligand binding site composition:

B-Factor:	20.461
Number of residues:	25
Including
Standard Amino Acids:	25
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.945	621.000

% Hydrophobic	% Polar
54.35	45.65
According to VolSite

Ligand :

HET Code:	2FA
Formula:	C10H12FN5O4
Molecular weight:	285.232 g/mol
DrugBank ID:	DB04441
Buried Surface Area:	61.49 %
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
74.9705	34.2191	-4.7637

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
C3'	CG	MET- 64	4.31	0	Hydrophobic	false
C5'	SD	MET- 64	3.8	0	Hydrophobic	false
F	CB	ALA- 156	4.32	0	Hydrophobic	false
C5'	CD2	PHE- 159	3.73	0	Hydrophobic	false
F	CD2	PHE- 159	3.5	0	Hydrophobic	false
F	CG1	VAL- 178	4.03	0	Hydrophobic	false
C2'	CB	GLU- 179	4.1	0	Hydrophobic	false
F	CG	MET- 180	3.62	0	Hydrophobic	false
C2'	CB	MET- 180	3.95	0	Hydrophobic	false
C3'	SD	MET- 180	3.76	0	Hydrophobic	false
O2'	N	MET- 180	2.9	135.27	H-Bond (Protein Donor)	false
O2'	OE2	GLU- 181	2.83	137.19	H-Bond (Ligand Donor)	false
O3'	OE1	GLU- 181	2.68	160.07	H-Bond (Ligand Donor)	false
N6	OD1	ASP- 204	3.34	136.48	H-Bond (Ligand Donor)	false