scPDB - 4g2j entry

Protein Data Bank Entry:

PDB ID : 4g2j

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2012-07-12

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:	40.566
Number of residues:	35
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	2
Water Molecules:	2
Cofactors:
Metals:	ZN MG

Cavity properties

Ligandability	Volume (Å3)
1.035	803.250

% Hydrophobic	% Polar
51.26	48.74
According to VolSite

Ligand :

HET Code:	0WF
Formula:	C21H26N5O2
Molecular weight:	380.463 g/mol
DrugBank ID:	-
Buried Surface Area:	47.23 %
Polar Surface area:	72.95 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	2
Rings:	5
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
74.9316	51.8422	40.7288

Binding mode :

What is Poseview ?

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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
C9	CE2	PHE- 251	4.38	0	Hydrophobic	false
C11	CG	MET- 365	3.67	0	Hydrophobic	false
C12	CG2	ILE- 403	3.99	0	Hydrophobic	false
C1	CD2	LEU- 420	4.03	0	Hydrophobic	false
C9	CD2	LEU- 420	3.97	0	Hydrophobic	false
C1	CD2	LEU- 421	4.35	0	Hydrophobic	false
C1	CE2	TYR- 424	3.78	0	Hydrophobic	false
N5	OH	TYR- 424	3.24	149.98	H-Bond (Ligand Donor)	false
C14	CD1	PHE- 441	3.74	0	Hydrophobic	false
C1	CB	ALA- 452	3.93	0	Hydrophobic	false
N1	OE1	GLN- 453	2.72	174.63	H-Bond (Ligand Donor)	false
O1	NE2	GLN- 453	2.98	173.56	H-Bond (Protein Donor)	false
C12	CZ	PHE- 456	4.43	0	Hydrophobic	false
C16	CB	PHE- 456	4.19	0	Hydrophobic	false
C19	CG2	VAL- 460	3.58	0	Hydrophobic	false
O1	O	HOH- 1022	2.85	160.05	H-Bond (Protein Donor)	false