scPDB - 4kp6 entry

Protein Data Bank Entry:

PDB ID : 4kp6

Resolution :1.500 Å

Experimental Method : X-ray

Deposition Date : 2013-05-13

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:	14.743
Number of residues:	32
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	2
Water Molecules:	2
Cofactors:
Metals:	MG ZN

Cavity properties

Ligandability	Volume (Å3)
0.991	749.250

% Hydrophobic	% Polar
50.90	49.10
According to VolSite

Ligand :

HET Code:	1S1
Formula:	C12H17N9
Molecular weight:	287.324 g/mol
DrugBank ID:	-
Buried Surface Area:	63.88 %
Polar Surface area:	117.22 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	2
Rings:	2
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
-41.2431	91.1046	114.958

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
C19	CE1	TYR- 233	4.37	0	Hydrophobic	false
C17	CG	MET- 347	3.45	0	Hydrophobic	false
C16	CD2	LEU- 393	4.04	0	Hydrophobic	false
N13	OD1	ASN- 395	2.88	167.13	H-Bond (Ligand Donor)	false
C14	CB	ASN- 395	4.02	0	Hydrophobic	false
C14	CE1	TYR- 403	3.81	0	Hydrophobic	false
C14	CB	TRP- 406	4.23	0	Hydrophobic	false
C14	CB	THR- 407	4.41	0	Hydrophobic	false
C14	CG2	ILE- 410	3.86	0	Hydrophobic	false
C19	CD1	ILE- 410	3.61	0	Hydrophobic	false
N11	NE2	GLN- 443	2.98	120.57	H-Bond (Protein Donor)	false
DuAr	DuAr	PHE- 446	3.88	0	Aromatic Face/Face	false
DuAr	DuAr	PHE- 446	3.86	0	Aromatic Face/Face	false
DuAr	DuAr	PHE- 446	3.86	0	Aromatic Face/Face	false
N5	O	HOH- 604	3.29	131.35	H-Bond (Protein Donor)	false
N1	O	HOH- 646	2.84	151.59	H-Bond (Ligand Donor)	false