scPDB - 2fm5 entry

Protein Data Bank Entry:

PDB ID : 2fm5

Resolution :2.030 Å

Experimental Method : X-ray

Deposition Date : 2006-01-07

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
B	100 %

Ligand binding site composition:

B-Factor:	26.782
Number of residues:	41
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	2
Water Molecules:	2
Cofactors:
Metals:	ZN MG

Cavity properties

Ligandability	Volume (Å3)
1.286	759.375

% Hydrophobic	% Polar
60.44	39.56
According to VolSite

Ligand :

HET Code:	M99
Formula:	C23H18F8N2O4S
Molecular weight:	570.452 g/mol
DrugBank ID:	-
Buried Surface Area:	55.95 %
Polar Surface area:	105.28 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	1
Rings:	4
Aromatic rings:	3
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
17.8561	-2.27497	-11.1406

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
F1	CE1	TYR- 159	4.43	0	Hydrophobic	false
F7	CE	MET- 273	4.42	0	Hydrophobic	false
F10	CB	MET- 273	3.35	0	Hydrophobic	false
F8	CG	MET- 273	3.74	0	Hydrophobic	false
C21	CG	MET- 273	3.66	0	Hydrophobic	false
C18	CD2	LEU- 319	4.26	0	Hydrophobic	false
C20	CD2	LEU- 319	3.93	0	Hydrophobic	false
F2	CB	ASN- 321	3.26	0	Hydrophobic	false
F2	CG	PRO- 322	3.4	0	Hydrophobic	false
C1	CE1	TYR- 329	3.68	0	Hydrophobic	false
F1	CB	TRP- 332	3.4	0	Hydrophobic	false
F1	CB	THR- 333	4.18	0	Hydrophobic	false
C2	CG2	ILE- 336	3.71	0	Hydrophobic	false
C9	CD1	ILE- 336	4.37	0	Hydrophobic	false
F1	CG2	ILE- 336	3.89	0	Hydrophobic	false
C5	CG1	ILE- 336	3.84	0	Hydrophobic	false
C8	CE2	PHE- 340	4.4	0	Hydrophobic	false
C12	SD	MET- 357	3.27	0	Hydrophobic	false
F6	CE	MET- 357	3.53	0	Hydrophobic	false
C12	CB	SER- 368	4	0	Hydrophobic	false
O1	NE2	GLN- 369	3.06	137.52	H-Bond (Protein Donor)	false
O2	NE2	GLN- 369	2.91	145.14	H-Bond (Protein Donor)	false
C12	CB	PHE- 372	4.08	0	Hydrophobic	false
F6	CD1	PHE- 372	4.42	0	Hydrophobic	false
F2	CE2	PHE- 372	3.6	0	Hydrophobic	false
C13	CG	PHE- 372	3.45	0	Hydrophobic	false
C16	CD1	ILE- 376	4.22	0	Hydrophobic	false
F7	CG1	ILE- 376	4.41	0	Hydrophobic	false
O4	O	HOH- 609	3.42	164.52	H-Bond (Protein Donor)	false