scPDB - 3itu entry

Protein Data Bank Entry:

PDB ID : 3itu

Resolution :1.580 Å

Experimental Method : X-ray

Deposition Date : 2009-08-28

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	cGMP-dependent 3',5'-cyclic phosphodiesterase
ID:	PDE2A_HUMAN
AC:	O00408
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.1.4.17

Chains:

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

Ligand binding site composition:

B-Factor:	16.271
Number of residues:	23
Including
Standard Amino Acids:	22
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.141	722.250

% Hydrophobic	% Polar
58.41	41.59
According to VolSite

Ligand :

HET Code:	IBM
Formula:	C10H14N4O2
Molecular weight:	222.244 g/mol
DrugBank ID:	DB07954
Buried Surface Area:	59.9 %
Polar Surface area:	69.3 Å2

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

Mass center Coordinates

X	Y	Z
36.6416	29.6636	-7.83737

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
C13	CE2	TYR- 655	3.84	0	Hydrophobic	false
C11	CD1	LEU- 770	4.12	0	Hydrophobic	false
C10	CG	GLN- 812	4.08	0	Hydrophobic	false
C10	CG2	ILE- 822	4.24	0	Hydrophobic	false
C10	CD1	ILE- 826	3.7	0	Hydrophobic	false
C13	CD1	ILE- 826	4.31	0	Hydrophobic	false
C12	CZ	PHE- 830	3.89	0	Hydrophobic	false
N7	OE1	GLN- 859	3.21	158.56	H-Bond (Ligand Donor)	false
C10	CE2	PHE- 862	4.1	0	Hydrophobic	false
C11	CE1	PHE- 862	4.02	0	Hydrophobic	false
DuAr	DuAr	PHE- 862	3.63	0	Aromatic Face/Face	false