scPDB - 3w5e entry

Protein Data Bank Entry:

PDB ID : 3w5e

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2013-01-28

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 4B
ID:	PDE4B_HUMAN
AC:	Q07343
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:	48.193
Number of residues:	40
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:	CA

Cavity properties

Ligandability	Volume (Å3)
1.290	918.000

% Hydrophobic	% Polar
59.19	40.81
According to VolSite

Ligand :

HET Code:	NVW
Formula:	C25H28N4O3S
Molecular weight:	464.580 g/mol
DrugBank ID:	-
Buried Surface Area:	62.67 %
Polar Surface area:	109.42 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	2
Rings:	4
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
24.7014	18.1372	-18.4253

Binding mode :

What is Poseview ?

2D View
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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
C11	CE1	TYR- 233	3.79	0	Hydrophobic	false
C25	CB	SER- 282	3.99	0	Hydrophobic	false
C15	CE	MET- 347	3.68	0	Hydrophobic	false
C12	CB	ASN- 395	4	0	Hydrophobic	false
C12	CE1	TYR- 403	3.79	0	Hydrophobic	false
C11	CB	TRP- 406	3.98	0	Hydrophobic	false
C13	CB	THR- 407	4.38	0	Hydrophobic	false
C10	CG2	ILE- 410	4.15	0	Hydrophobic	false
C13	CG2	ILE- 410	3.94	0	Hydrophobic	false
C17	CD1	ILE- 410	3.83	0	Hydrophobic	false
C23	CZ	PHE- 414	4.26	0	Hydrophobic	false
C24	CE1	PHE- 414	3.75	0	Hydrophobic	false
C5	CB	SER- 442	3.51	0	Hydrophobic	false
N1	NE2	GLN- 443	2.88	177.57	H-Bond (Protein Donor)	false
C13	CE2	PHE- 446	4.18	0	Hydrophobic	false
C3	CB	PHE- 446	4.13	0	Hydrophobic	false
DuAr	DuAr	PHE- 446	3.72	0	Aromatic Face/Face	false
DuAr	DuAr	PHE- 446	3.72	0	Aromatic Face/Face	false
C6	CB	LEU- 502	3.69	0	Hydrophobic	false
C6	CE	MET- 503	3.45	0	Hydrophobic	false
C7	CB	PHE- 506	3.9	0	Hydrophobic	false
C23	CB	PHE- 506	3.65	0	Hydrophobic	false
O1	O	HOH- 1050	2.88	175.24	H-Bond (Protein Donor)	false