scPDB - 3tvx entry

Protein Data Bank Entry:

PDB ID : 3tvx

Resolution :2.840 Å

Experimental Method : X-ray

Deposition Date : 2011-09-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	cAMP-specific 3',5'-cyclic phosphodiesterase 4A
ID:	PDE4A_HUMAN
AC:	P27815
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.1.4.53

Chains:

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

Ligand binding site composition:

B-Factor:	65.607
Number of residues:	24
Including
Standard Amino Acids:	24
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.166	840.375

% Hydrophobic	% Polar
55.02	44.98
According to VolSite

Ligand :

HET Code:	PNX
Formula:	C13H18N4O3
Molecular weight:	278.307 g/mol
DrugBank ID:	DB00806
Buried Surface Area:	60.85 %
Polar Surface area:	75.51 Å2

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

Mass center Coordinates

X	Y	Z
43.495	16.6444	-24.5736

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
CAH	CZ	TYR- 371	3.85	0	Hydrophobic	false
CAB	CE	MET- 485	4.02	0	Hydrophobic	false
CAI	CD2	LEU- 531	3.93	0	Hydrophobic	false
CAA	CB	ASN- 533	3.84	0	Hydrophobic	false
CAA	CE1	TYR- 541	4.01	0	Hydrophobic	false
CAA	CB	TRP- 544	4.11	0	Hydrophobic	false
CAA	CG2	ILE- 548	4.06	0	Hydrophobic	false
CAJ	CG1	ILE- 548	3.7	0	Hydrophobic	false
CAH	CD1	ILE- 548	4.03	0	Hydrophobic	false
CAK	CD1	ILE- 548	3.92	0	Hydrophobic	false
CAK	CZ	PHE- 552	4.07	0	Hydrophobic	false
CAC	SD	MET- 569	3.59	0	Hydrophobic	false
CAC	CB	SER- 580	4.19	0	Hydrophobic	false
O2	NE2	GLN- 581	3.5	146.93	H-Bond (Protein Donor)	false
CAB	CE1	PHE- 584	4.31	0	Hydrophobic	false
CAC	CB	PHE- 584	3.73	0	Hydrophobic	false
CAI	CZ	PHE- 584	3.63	0	Hydrophobic	false