scPDB - 2yy2 entry

Protein Data Bank Entry:

PDB ID : 2yy2

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2007-04-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A
ID:	PDE9A_HUMAN
AC:	O76083
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	34.344
Number of residues:	22
Including
Standard Amino Acids:	21
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.987	772.875

% Hydrophobic	% Polar
49.34	50.66
According to VolSite

Ligand :

HET Code:	IBM
Formula:	C10H14N4O2
Molecular weight:	222.244 g/mol
DrugBank ID:	DB07954
Buried Surface Area:	41.62 %
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
77.4224	51.5457	41.1275

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
C10	CZ	PHE- 251	4.15	0	Hydrophobic	false
C13	CG	MET- 365	3.65	0	Hydrophobic	false
C10	CB	ILE- 403	4.22	0	Hydrophobic	false
C14	CD1	LEU- 420	4.2	0	Hydrophobic	false
N9	OH	TYR- 424	3.43	149.49	H-Bond (Protein Donor)	false
C14	CZ	TYR- 424	3.79	0	Hydrophobic	false
N7	OE1	GLN- 453	3.22	159.47	H-Bond (Ligand Donor)	false
O6	NE2	GLN- 453	3.43	145.58	H-Bond (Protein Donor)	false
C10	CE2	PHE- 456	4.06	0	Hydrophobic	false
C11	CE1	PHE- 456	4.38	0	Hydrophobic	false
DuAr	DuAr	PHE- 456	3.85	0	Aromatic Face/Face	false