scPDB - 1a9p entry

Protein Data Bank Entry:

PDB ID : 1a9p

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 1998-04-10

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
A	100 %

Ligand binding site composition:

B-Factor:	9.741
Number of residues:	33
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.769	506.250

% Hydrophobic	% Polar
40.00	60.00
According to VolSite

Ligand :

HET Code:	9DI
Formula:	C11H13N3O5
Molecular weight:	267.238 g/mol
DrugBank ID:	DB02796
Buried Surface Area:	76.87 %
Polar Surface area:	127.17 Å2

Number of
H-Bond Acceptors:	6
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
22.3511	90.2426	74.7499

Binding mode :

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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
C4'	CB	SER- 33	4.4	0	Hydrophobic	false
C3'	CE2	TYR- 88	4.14	0	Hydrophobic	false
O3'	OH	TYR- 88	2.79	158.84	H-Bond (Protein Donor)	false
C1'	CB	ALA- 116	4.48	0	Hydrophobic	false
C5'	CZ	PHE- 200	3.99	0	Hydrophobic	false
N1	OE2	GLU- 201	3.3	120.29	H-Bond (Ligand Donor)	false
N1	OE1	GLU- 201	3	169.1	H-Bond (Ligand Donor)	false
C2'	CG	MET- 219	3.79	0	Hydrophobic	false
C3'	SD	MET- 219	3.91	0	Hydrophobic	false
O2'	N	MET- 219	2.8	133.28	H-Bond (Protein Donor)	false
O6	ND2	ASN- 243	3.06	167.29	H-Bond (Protein Donor)	false
N7	OD1	ASN- 243	2.92	174.91	H-Bond (Ligand Donor)	false
O5'	ND1	HIS- 257	2.8	156.3	H-Bond (Ligand Donor)	false