scPDB - 3bgs entry

Protein Data Bank Entry:

PDB ID : 3bgs

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2007-11-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	9.420	9.420	9.420	0.000	9.420	2

List of CHEMBLId :

CHEMBL454743

Binding Site :

Uniprot Annotation

Name:	Purine nucleoside phosphorylase
ID:	PNPH_HUMAN
AC:	P00491
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.4.2.1

Chains:

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

Ligand binding site composition:

B-Factor:	49.138
Number of residues:	29
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.083	354.375

% Hydrophobic	% Polar
47.62	52.38
According to VolSite

Ligand :

HET Code:	DIH
Formula:	C12H20N4O3
Molecular weight:	268.312 g/mol
DrugBank ID:	DB03551
Buried Surface Area:	69.14 %
Polar Surface area:	102.97 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	5
Rings:	3
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	2
Rule of Five Violation:	0
Rotatable Bonds:	3

Mass center Coordinates

X	Y	Z
14.7146	11.2302	57.6372

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
O3'	OH	TYR- 88	2.91	147.69	H-Bond (Protein Donor)	false
C5'	CZ	PHE- 200	3.79	0	Hydrophobic	false
N1	OE2	GLU- 201	3.19	120.6	H-Bond (Ligand Donor)	false
N1	OE1	GLU- 201	2.79	172.47	H-Bond (Ligand Donor)	false
C4'	SD	MET- 219	4.06	0	Hydrophobic	false
N7	OD1	ASN- 243	2.76	167.5	H-Bond (Ligand Donor)	false
O6	ND2	ASN- 243	3.02	176.25	H-Bond (Protein Donor)	false
O5'	ND1	HIS- 257	3.27	166.96	H-Bond (Ligand Donor)	false