scPDB - 1y2k entry

Protein Data Bank Entry:

PDB ID : 1y2k

Resolution :1.360 Å

Experimental Method : X-ray

Deposition Date : 2004-11-22

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 4D
ID:	PDE4D_HUMAN
AC:	Q08499
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:	9.284
Number of residues:	29
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	2
Water Molecules:	0
Cofactors:
Metals:	ZN MG

Cavity properties

Ligandability	Volume (Å3)
1.150	786.375

% Hydrophobic	% Polar
60.09	39.91
According to VolSite

Ligand :

HET Code:	7DE
Formula:	C14H15N3O4
Molecular weight:	289.287 g/mol
DrugBank ID:	DB01959
Buried Surface Area:	64.14 %
Polar Surface area:	89.94 Å2

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

Mass center Coordinates

X	Y	Z
13.2935	45.0121	13.2356

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
C6	CZ	TYR- 159	3.76	0	Hydrophobic	false
C11	CG	MET- 273	4.22	0	Hydrophobic	false
C13	CG	MET- 273	3.77	0	Hydrophobic	false
C11	CD2	LEU- 319	4.03	0	Hydrophobic	false
C17	CB	ASN- 321	3.84	0	Hydrophobic	false
C17	CE1	TYR- 329	4.03	0	Hydrophobic	false
C17	CB	TRP- 332	3.84	0	Hydrophobic	false
C17	CB	THR- 333	4.4	0	Hydrophobic	false
C6	CD1	ILE- 336	4.05	0	Hydrophobic	false
C16	CG2	ILE- 336	3.75	0	Hydrophobic	false
C9	CE2	PHE- 340	4.18	0	Hydrophobic	false
C9	SD	MET- 357	3.74	0	Hydrophobic	false
O18	NE2	GLN- 369	2.9	168.71	H-Bond (Protein Donor)	false
C9	CD1	PHE- 372	3.64	0	Hydrophobic	false
C16	CE2	PHE- 372	4.02	0	Hydrophobic	false