scPDB - 1jdz entry

Protein Data Bank Entry:

PDB ID : 1jdz

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2001-06-15

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_SULSO
AC:	P50389
Organism:	Sulfolobus solfataricus
Reign:	Archaea
TaxID:	273057
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
B	86 %
C	14 %

Ligand binding site composition:

B-Factor:	21.950
Number of residues:	28
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.416	567.000

% Hydrophobic	% Polar
42.26	57.74
According to VolSite

Ligand :

HET Code:	FMB
Formula:	C10H12N4O5
Molecular weight:	268.226 g/mol
DrugBank ID:	DB04198
Buried Surface Area:	69.18 %
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
67.5555	110.458	33.8845

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
O5'	NE2	HIS- 5	2.86	145.42	H-Bond (Ligand Donor)	false
C3'	CG2	ILE- 64	4.21	0	Hydrophobic	false
C5'	CD1	ILE- 64	4.35	0	Hydrophobic	false
N3	OG1	THR- 89	3.25	169.29	H-Bond (Ligand Donor)	false
C2'	CG	GLU- 180	4.29	0	Hydrophobic	false
C2'	CG	MET- 181	3.89	0	Hydrophobic	false
C3'	SD	MET- 181	3.79	0	Hydrophobic	false
O3'	OE2	GLU- 182	3.43	142.3	H-Bond (Protein Donor)	false
O3'	OE1	GLU- 182	3.26	148.58	H-Bond (Ligand Donor)	false
N1	OD1	ASP- 205	2.83	163.26	H-Bond (Protein Donor)	false