scPDB - 1mkd entry

Protein Data Bank Entry:

PDB ID : 1mkd

Resolution :2.900 Å

Experimental Method : X-ray

Deposition Date : 2002-08-29

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
E	96 %
J	4 %

Ligand binding site composition:

B-Factor:	39.746
Number of residues:	25
Including
Standard Amino Acids:	25
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.240	1474.875

% Hydrophobic	% Polar
53.55	46.45
According to VolSite

Ligand :

HET Code:	ZAR
Formula:	C12H10F2N2O3
Molecular weight:	268.216 g/mol
DrugBank ID:	DB02918
Buried Surface Area:	56.4 %
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
93.8797	10.8405	77.1305

Binding mode :

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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
F17	CE1	TYR- 256	3.92	0	Hydrophobic	false
C14	CB	ASN- 418	4.24	0	Hydrophobic	false
F16	CG	PRO- 419	3.75	0	Hydrophobic	false
F16	CE1	TYR- 426	3.5	0	Hydrophobic	false
F17	CB	TRP- 429	3.6	0	Hydrophobic	false
F17	CB	THR- 430	4.32	0	Hydrophobic	false
C11	CG2	ILE- 433	3.96	0	Hydrophobic	false
F17	CG2	ILE- 433	3.55	0	Hydrophobic	false
C13	CG1	ILE- 433	4.03	0	Hydrophobic	false
C19	CE	MET- 454	3.44	0	Hydrophobic	false
O15	NE2	GLN- 466	3.36	137.68	H-Bond (Protein Donor)	false
O18	NE2	GLN- 466	2.98	139.61	H-Bond (Protein Donor)	false
F16	CE2	PHE- 469	4.26	0	Hydrophobic	false
C19	CB	PHE- 469	3.64	0	Hydrophobic	false
DuAr	DuAr	PHE- 469	3.91	0	Aromatic Face/Face	false