scPDB - 3zbr entry

Protein Data Bank Entry:

PDB ID : 3zbr

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2012-11-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	2',3'-cyclic-nucleotide 3'-phosphodiesterase
ID:	CN37_MOUSE
AC:	P16330
Organism:	Mus musculus
Reign:	Eukaryota
TaxID:	10090
EC Number:	3.1.4.37

Chains:

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

Ligand binding site composition:

B-Factor:	34.499
Number of residues:	29
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.127	1090.125

% Hydrophobic	% Polar
43.65	56.35
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	34.98 %
Polar Surface area:	405.54 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	5
Rings:	5
Aromatic rings:	3
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
57.5199	-7.37677	56.4116

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
C5B	CD2	LEU- 167	3.4	0	Hydrophobic	false
C5D	CD2	LEU- 167	3.64	0	Hydrophobic	false
C3D	CD2	LEU- 167	4.4	0	Hydrophobic	false
C4B	CD1	TYR- 168	3.45	0	Hydrophobic	false
O2B	OG1	THR- 232	3.14	163.71	H-Bond (Protein Donor)	false
O2X	OG1	THR- 232	3.42	123.61	H-Bond (Protein Donor)	false
C1B	CG2	THR- 232	4.29	0	Hydrophobic	false
C5B	CE1	PHE- 235	3.75	0	Hydrophobic	false
C4B	CD1	PHE- 235	4.24	0	Hydrophobic	false
C1B	CD1	PHE- 235	4.03	0	Hydrophobic	false
O1X	OG1	THR- 311	2.81	150.2	H-Bond (Protein Donor)	false
C3D	CE2	TYR- 376	3.8	0	Hydrophobic	false
C2D	CZ	TYR- 376	3.64	0	Hydrophobic	false
O2X	O	HOH- 2021	2.77	179.96	H-Bond (Protein Donor)	false
O3X	O	HOH- 2038	3.37	179.95	H-Bond (Protein Donor)	false