scPDB - 3dy8 entry

Protein Data Bank Entry:

PDB ID : 3dy8

Resolution :2.150 Å

Experimental Method : X-ray

Deposition Date : 2008-07-25

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:	38.566
Number of residues:	33
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	2
Water Molecules:	2
Cofactors:
Metals:	MN MG

Cavity properties

Ligandability	Volume (Å3)
1.027	762.750

% Hydrophobic	% Polar
47.79	52.21
According to VolSite

Ligand :

HET Code:	5GP
Formula:	C10H12N5O8P
Molecular weight:	361.205 g/mol
DrugBank ID:	-
Buried Surface Area:	59.14 %
Polar Surface area:	217.22 Å2

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

Mass center Coordinates

X	Y	Z
78.4195	50.171	41.5333

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
O1P	NE2	HIS- 252	2.53	133.63	H-Bond (Protein Donor)	false
O3P	NE2	HIS- 252	3.42	130.67	H-Bond (Protein Donor)	false
C4'	CG	MET- 365	3.7	0	Hydrophobic	false
C5'	CG2	ILE- 403	3.69	0	Hydrophobic	false
C2'	CD1	LEU- 420	4.13	0	Hydrophobic	false
C2'	CZ	TYR- 424	4.35	0	Hydrophobic	false
N2	O	ALA- 452	3.46	143.11	H-Bond (Ligand Donor)	false
O6	NE2	GLN- 453	2.86	177.26	H-Bond (Protein Donor)	false
N1	OE1	GLN- 453	2.57	165.62	H-Bond (Ligand Donor)	false
N2	OE1	GLN- 453	3.35	123.9	H-Bond (Ligand Donor)	false
C1'	CZ	PHE- 456	4.13	0	Hydrophobic	false
O2P	MN	MN- 901	2.51	0	Metal Acceptor	false
O3P	MN	MN- 901	2.69	0	Metal Acceptor	false
O2P	MG	MG- 902	2.18	0	Metal Acceptor	false
N7	O	HOH- 963	3.32	164.55	H-Bond (Protein Donor)	false
O2'	O	HOH- 1100	3.34	129.55	H-Bond (Protein Donor)	false