scPDB - 3g45 entry

Protein Data Bank Entry:

PDB ID : 3g45

Resolution :2.630 Å

Experimental Method : X-ray

Deposition Date : 2009-02-03

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:	29.824
Number of residues:	35
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	2
Water Molecules:	0
Cofactors:
Metals:	ZN MG

Cavity properties

Ligandability	Volume (Å3)
1.403	1029.375

% Hydrophobic	% Polar
51.48	48.52
According to VolSite

Ligand :

HET Code:	988
Formula:	C21H15N3O2
Molecular weight:	341.363 g/mol
DrugBank ID:	-
Buried Surface Area:	71.01 %
Polar Surface area:	71.59 Å2

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

Mass center Coordinates

X	Y	Z
2.03392	35.4683	16.6449

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
C43	CG2	THR- 278	3.84	0	Hydrophobic	false
C35	CZ	PHE- 279	4.37	0	Hydrophobic	false
C43	CG	MET- 519	3.67	0	Hydrophobic	false
C35	CE	MET- 519	3.36	0	Hydrophobic	false
C35	CD2	LEU- 565	3.9	0	Hydrophobic	false
C6	CB	ASN- 567	4.02	0	Hydrophobic	false
C19	CG2	ILE- 582	4.49	0	Hydrophobic	false
C28	CG2	ILE- 582	4.2	0	Hydrophobic	false
C39	CD1	ILE- 582	3.92	0	Hydrophobic	false
C6	CG2	ILE- 582	3.92	0	Hydrophobic	false
C27	SD	MET- 583	3.71	0	Hydrophobic	false
C26	SD	MET- 603	4.03	0	Hydrophobic	false
C27	CG	MET- 603	4.46	0	Hydrophobic	false
C26	CB	SER- 614	3.8	0	Hydrophobic	false
N4	NE2	GLN- 615	2.87	148.98	H-Bond (Protein Donor)	false
C35	CZ	PHE- 618	4.33	0	Hydrophobic	false
C24	CG	PHE- 618	3.48	0	Hydrophobic	false
DuAr	DuAr	PHE- 618	3.98	0	Aromatic Face/Face	false
DuAr	DuAr	PHE- 618	3.98	0	Aromatic Face/Face	false