scPDB - 1xor entry

Protein Data Bank Entry:

PDB ID : 1xor

Resolution :1.540 Å

Experimental Method : X-ray

Deposition Date : 2004-10-06

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:	9.885
Number of residues:	27
Including
Standard Amino Acids:	24
Non Standard Amino Acids:	2
Water Molecules:	1
Cofactors:
Metals:	ZN MG

Cavity properties

Ligandability	Volume (Å3)
1.076	796.500

% Hydrophobic	% Polar
55.93	44.07
According to VolSite

Ligand :

HET Code:	ZAR
Formula:	C12H10F2N2O3
Molecular weight:	268.216 g/mol
DrugBank ID:	DB02918
Buried Surface Area:	72.47 %
Polar Surface area:	59.92 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	1
Rings:	2
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
6.24411	-2.16547	56.9404

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- 159	4.44	0	Hydrophobic	false
N3	NE2	HIS- 160	2.53	147.52	H-Bond (Protein Donor)	false
N4	NE2	HIS- 160	3.39	134.42	H-Bond (Protein Donor)	false
C6	CD2	LEU- 319	3.77	0	Hydrophobic	false
C19	CB	ASN- 321	4.21	0	Hydrophobic	false
C19	CB	TRP- 332	4.45	0	Hydrophobic	false
C19	CG2	ILE- 336	3.83	0	Hydrophobic	false
C10	CG2	ILE- 336	3.8	0	Hydrophobic	false
C8	CG1	ILE- 336	3.94	0	Hydrophobic	false
F17	SD	MET- 337	4.44	0	Hydrophobic	false
F16	CE2	PHE- 340	4.4	0	Hydrophobic	false
F17	CE2	PHE- 340	4.19	0	Hydrophobic	false
F17	SD	MET- 357	3.25	0	Hydrophobic	false
F17	CB	SER- 368	3.84	0	Hydrophobic	false
O15	NE2	GLN- 369	2.9	139.94	H-Bond (Protein Donor)	false
O18	NE2	GLN- 369	3.29	150.78	H-Bond (Protein Donor)	false
C19	CE2	PHE- 372	4.35	0	Hydrophobic	false
C14	CG	PHE- 372	3.63	0	Hydrophobic	false
C10	CE2	PHE- 372	3.43	0	Hydrophobic	false
O1	ZN	ZN- 1001	2.16	0	Metal Acceptor	false