scPDB - 1a69 entry

Protein Data Bank Entry:

PDB ID : 1a69

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 1998-03-08

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_ECOLI
AC:	P0ABP8
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	15 %
C	85 %

Ligand binding site composition:

B-Factor:	21.086
Number of residues:	25
Including
Standard Amino Acids:	25
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.646	563.625

% Hydrophobic	% Polar
53.89	46.11
According to VolSite

Ligand :

HET Code:	FMB
Formula:	C10H12N4O5
Molecular weight:	268.226 g/mol
DrugBank ID:	DB04198
Buried Surface Area:	66.14 %
Polar Surface area:	140.06 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	5
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
-8.02358	82.7508	85.5372

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	4.34	0	Hydrophobic	false
C5'	SD	MET- 64	3.8	0	Hydrophobic	false
N8	OG	SER- 90	3.34	165.06	H-Bond (Protein Donor)	false
C5'	CE2	PHE- 159	3.85	0	Hydrophobic	false
C2'	CB	GLU- 179	4.04	0	Hydrophobic	false
C2'	CG	MET- 180	3.81	0	Hydrophobic	false
C3'	SD	MET- 180	3.61	0	Hydrophobic	false
O2'	N	MET- 180	3.46	139.33	H-Bond (Protein Donor)	false
O2'	OE1	GLU- 181	2.57	170.94	H-Bond (Protein Donor)	false
O3'	OE2	GLU- 181	2.69	148.89	H-Bond (Ligand Donor)	false