scPDB - 3wd9 entry

Protein Data Bank Entry:

PDB ID : 3wd9

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2013-06-11

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
B	100 %

Ligand binding site composition:

B-Factor:	45.447
Number of residues:	41
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	2
Water Molecules:	1
Cofactors:
Metals:	ZN CA

Cavity properties

Ligandability	Volume (Å3)
1.253	907.875

% Hydrophobic	% Polar
56.88	43.12
According to VolSite

Ligand :

HET Code:	QPC
Formula:	C24H27N5O2
Molecular weight:	417.503 g/mol
DrugBank ID:	-
Buried Surface Area:	64.42 %
Polar Surface area:	110 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	3
Rings:	3
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
19.2612	-21.0249	-12.4077

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
C17	CG	MET- 347	3.77	0	Hydrophobic	false
C14	CG	MET- 347	3.82	0	Hydrophobic	false
C11	CD2	LEU- 393	4.45	0	Hydrophobic	false
N5	OD1	ASN- 395	2.96	160.88	H-Bond (Ligand Donor)	false
C4	CD1	ILE- 410	3.68	0	Hydrophobic	false
C22	CG1	ILE- 410	4.37	0	Hydrophobic	false
C11	CD1	ILE- 410	3.73	0	Hydrophobic	false
C22	CG	GLU- 413	3.84	0	Hydrophobic	false
C24	CG	GLU- 413	4.3	0	Hydrophobic	false
C21	CE2	PHE- 414	3.99	0	Hydrophobic	false
C22	CZ	PHE- 414	3.66	0	Hydrophobic	false
C24	CD2	PHE- 414	4.09	0	Hydrophobic	false
C24	CB	GLN- 417	3.84	0	Hydrophobic	false
C7	CB	SER- 442	3.84	0	Hydrophobic	false
N1	NE2	GLN- 443	2.91	166.45	H-Bond (Protein Donor)	false
DuAr	DuAr	PHE- 446	3.88	0	Aromatic Face/Face	false
C6	CB	PHE- 446	3.5	0	Hydrophobic	false
C8	CB	LEU- 502	3.85	0	Hydrophobic	false
C8	SD	MET- 503	3.76	0	Hydrophobic	false
C9	CB	PHE- 506	3.71	0	Hydrophobic	false
O2	O	HOH- 1040	2.82	164.45	H-Bond (Protein Donor)	false