scPDB - 1lv8 entry

Protein Data Bank Entry:

PDB ID : 1lv8

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2002-05-27

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
ID:	PNPH_BOVIN
AC:	P55859
Organism:	Bos taurus
Reign:	Eukaryota
TaxID:	9913
EC Number:	2.4.2.1

Chains:

Chain Name:	Percentage of Residues within binding site
E	97 %
F	3 %

Ligand binding site composition:

B-Factor:	44.438
Number of residues:	33
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.762	347.625

% Hydrophobic	% Polar
56.31	43.69
According to VolSite

Ligand :

HET Code:	9PP
Formula:	C9H13N6O4P
Molecular weight:	300.211 g/mol
DrugBank ID:	DB02222
Buried Surface Area:	74.59 %
Polar Surface area:	177.86 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	2
Rings:	2
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
-72.7781	4.7115	272.641

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
C14	CB	SER- 33	3.62	0	Hydrophobic	false
O2P	N	SER- 33	2.73	163.79	H-Bond (Protein Donor)	false
O1P	NE2	HIS- 86	2.78	158.11	H-Bond (Protein Donor)	false
C14	CB	ALA- 116	3.94	0	Hydrophobic	false
O2P	N	ALA- 116	3.14	159.05	H-Bond (Protein Donor)	false
C12	CE2	PHE- 200	4.11	0	Hydrophobic	false
DuAr	DuAr	PHE- 200	3.9	0	Aromatic Face/Face	false
N1	OE1	GLU- 201	2.57	158.9	H-Bond (Ligand Donor)	false
N2	OE2	GLU- 201	2.54	159.13	H-Bond (Ligand Donor)	false
N2	OE1	GLU- 201	3.09	131.22	H-Bond (Ligand Donor)	false
C12	SD	MET- 219	4.38	0	Hydrophobic	false
O3P	OG	SER- 220	2.84	143.73	H-Bond (Protein Donor)	false
N7	ND2	ASN- 243	3.15	163.49	H-Bond (Protein Donor)	false
N6	OD1	ASN- 243	3.17	170.59	H-Bond (Ligand Donor)	false
C12	CE1	PHE- 1159	3.88	0	Hydrophobic	false