scPDB - 4wdb entry

Protein Data Bank Entry:

PDB ID : 4wdb

Resolution :1.600 Å

Experimental Method : X-ray

Deposition Date : 2014-09-08

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:	30.605
Number of residues:	22
Including
Standard Amino Acids:	21
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.411	840.375

% Hydrophobic	% Polar
60.64	39.36
According to VolSite

Ligand :

HET Code:	2AM
Formula:	C10H12N5O7P
Molecular weight:	345.205 g/mol
DrugBank ID:	-
Buried Surface Area:	46.44 %
Polar Surface area:	201.54 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
-7.81983	5.14061	-24.1265

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
C5'	CE2	TYR- 168	3.49	0	Hydrophobic	false
O3'	NE2	HIS- 230	2.74	168.18	H-Bond (Protein Donor)	false
O2P	OG1	THR- 232	3.07	155.37	H-Bond (Protein Donor)	false
C1'	CG2	THR- 232	3.91	0	Hydrophobic	false
C5'	CE1	PHE- 235	4.24	0	Hydrophobic	false
C1'	CD1	PHE- 235	4.48	0	Hydrophobic	false
DuAr	DuAr	PHE- 235	3.61	0	Aromatic Face/Face	false
O2P	NE2	HIS- 309	3.48	122.24	H-Bond (Protein Donor)	false
O3P	NE2	HIS- 309	2.66	171.93	H-Bond (Protein Donor)	false
O1P	OG1	THR- 311	3.2	145.8	H-Bond (Protein Donor)	false
O3P	OG1	THR- 311	2.71	130.52	H-Bond (Protein Donor)	false
C2'	CB	PRO- 320	3.56	0	Hydrophobic	false