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Chlorine in PDB 4wcu: PDE4 Complexed with Inhibitor

Enzymatic activity of PDE4 Complexed with Inhibitor

All present enzymatic activity of PDE4 Complexed with Inhibitor:
3.1.4.53;

Protein crystallography data

The structure of PDE4 Complexed with Inhibitor, PDB code: 4wcu was solved by M.D.Sorensen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 92.85 / 2.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 99.232, 113.545, 160.535, 90.00, 90.00, 90.00
R / Rfree (%) 24.4 / 30.4

Other elements in 4wcu:

The structure of PDE4 Complexed with Inhibitor also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Zinc (Zn) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the PDE4 Complexed with Inhibitor (pdb code 4wcu). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the PDE4 Complexed with Inhibitor, PDB code: 4wcu:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 4wcu

Go back to Chlorine Binding Sites List in 4wcu
Chlorine binding site 1 out of 8 in the PDE4 Complexed with Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of PDE4 Complexed with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl500

b:47.8
occ:1.00
 CL7 A:3KQ500 0.0 47.8 1.0
C6 A:3KQ500 1.8 46.7 1.0
C5 A:3KQ500 2.8 47.1 1.0
C1 A:3KQ500 2.8 46.4 1.0
C9 A:3KQ500 3.2 47.3 1.0
CE1 A:PHE340 3.6 37.5 1.0
C10 A:3KQ500 3.6 47.6 1.0
C30 A:3KQ500 3.6 53.6 1.0
CZ A:PHE340 3.7 37.7 1.0
O11 A:3KQ500 3.7 46.7 1.0
CE1 A:HIS160 3.8 33.6 1.0
C29 A:3KQ500 4.0 53.6 1.0
N4 A:3KQ500 4.0 47.0 1.0
C2 A:3KQ500 4.2 46.5 1.0
O A:HOH692 4.3 23.8 1.0
CD1 A:ILE336 4.3 35.4 1.0
NE2 A:HIS160 4.4 34.1 1.0
C3 A:3KQ500 4.6 47.2 1.0
C12 A:3KQ500 4.6 47.2 1.0
C31 A:3KQ500 4.7 53.3 1.0
ND1 A:HIS160 4.9 34.1 1.0
O22 A:3KQ500 4.9 48.5 1.0
CD1 A:PHE340 4.9 38.3 1.0

Chlorine binding site 2 out of 8 in 4wcu

Go back to Chlorine Binding Sites List in 4wcu
Chlorine binding site 2 out of 8 in the PDE4 Complexed with Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of PDE4 Complexed with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl500

b:46.4
occ:1.00
 CL8 A:3KQ500 0.0 46.4 1.0
C2 A:3KQ500 1.8 46.5 1.0
C3 A:3KQ500 2.8 47.2 1.0
C1 A:3KQ500 2.8 46.4 1.0
C9 A:3KQ500 3.2 47.3 1.0
OD2 A:ASP318 3.5 31.4 1.0
CD2 A:LEU319 3.8 34.4 1.0
CG A:ASP318 3.8 33.3 1.0
O A:HOH627 3.9 21.7 1.0
C10 A:3KQ500 3.9 47.6 1.0
N4 A:3KQ500 4.0 47.0 1.0
OD1 A:ASP318 4.1 32.9 1.0
O11 A:3KQ500 4.2 46.7 1.0
C6 A:3KQ500 4.2 46.7 1.0
CG A:LEU319 4.3 34.6 1.0
O A:ASP318 4.5 35.4 1.0
C5 A:3KQ500 4.6 47.1 1.0
CB A:ASP318 4.6 34.6 1.0
CG A:MET273 4.7 48.7 1.0
C A:ASP318 4.8 35.6 1.0
SD A:MET273 4.8 47.6 1.0
ZN A:ZN501 5.0 45.9 1.0
C12 A:3KQ500 5.0 47.2 1.0

Chlorine binding site 3 out of 8 in 4wcu

Go back to Chlorine Binding Sites List in 4wcu
Chlorine binding site 3 out of 8 in the PDE4 Complexed with Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of PDE4 Complexed with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl500

b:43.2
occ:1.00
 CL7 B:3KQ500 0.0 43.2 1.0
C6 B:3KQ500 1.8 44.4 1.0
C5 B:3KQ500 2.8 43.8 1.0
C1 B:3KQ500 2.8 44.0 1.0
C9 B:3KQ500 3.2 43.6 1.0
C10 B:3KQ500 3.5 42.2 1.0
O11 B:3KQ500 3.6 42.0 1.0
C30 B:3KQ500 3.6 52.9 1.0
C29 B:3KQ500 3.8 53.1 1.0
CE1 B:PHE340 3.8 37.1 1.0
CZ B:PHE340 3.9 37.3 1.0
CE1 B:HIS160 3.9 34.4 1.0
N4 B:3KQ500 4.0 44.1 1.0
C2 B:3KQ500 4.2 43.1 1.0
NE2 B:HIS160 4.5 35.1 1.0
C12 B:3KQ500 4.5 41.3 1.0
CD1 B:ILE336 4.5 33.6 1.0
C3 B:3KQ500 4.6 43.3 1.0
C31 B:3KQ500 4.7 53.0 1.0
O B:HOH633 4.7 42.1 1.0
ND1 B:HIS160 5.0 33.6 1.0
O22 B:3KQ500 5.0 42.8 1.0

Chlorine binding site 4 out of 8 in 4wcu

Go back to Chlorine Binding Sites List in 4wcu
Chlorine binding site 4 out of 8 in the PDE4 Complexed with Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of PDE4 Complexed with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl500

b:45.1
occ:1.00
 CL8 B:3KQ500 0.0 45.1 1.0
C2 B:3KQ500 1.8 43.1 1.0
C3 B:3KQ500 2.7 43.3 1.0
C1 B:3KQ500 2.8 44.0 1.0
OD2 B:ASP318 3.2 35.7 1.0
C9 B:3KQ500 3.2 43.6 1.0
O B:HOH638 3.5 29.2 1.0
CD2 B:LEU319 3.5 36.5 1.0
CG B:ASP318 3.6 36.2 1.0
OD1 B:ASP318 4.0 35.7 1.0
N4 B:3KQ500 4.0 44.1 1.0
C10 B:3KQ500 4.0 42.2 1.0
C6 B:3KQ500 4.2 44.4 1.0
O11 B:3KQ500 4.2 42.0 1.0
CG B:LEU319 4.3 37.0 1.0
CB B:ASP318 4.4 36.9 1.0
O B:ASP318 4.4 37.2 1.0
C5 B:3KQ500 4.6 43.8 1.0
C B:ASP318 4.6 37.7 1.0
CG B:MET273 4.8 48.0 1.0
O B:THR271 4.8 39.1 1.0
ZN B:ZN501 4.9 44.0 1.0

Chlorine binding site 5 out of 8 in 4wcu

Go back to Chlorine Binding Sites List in 4wcu
Chlorine binding site 5 out of 8 in the PDE4 Complexed with Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of PDE4 Complexed with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl500

b:45.1
occ:1.00
 CL7 C:3KQ500 0.0 45.1 1.0
C6 C:3KQ500 1.8 44.5 1.0
C5 C:3KQ500 2.8 45.4 1.0
C1 C:3KQ500 2.8 44.7 1.0
C9 C:3KQ500 3.2 44.2 1.0
C10 C:3KQ500 3.4 44.5 1.0
O11 C:3KQ500 3.4 43.8 1.0
CZ C:PHE340 3.5 35.0 1.0
C30 C:3KQ500 3.6 52.9 1.0
CE1 C:PHE340 3.7 34.8 1.0
C29 C:3KQ500 3.9 52.8 1.0
CE1 C:HIS160 4.0 34.1 1.0
N4 C:3KQ500 4.0 45.4 1.0
O C:HOH628 4.2 36.0 1.0
C2 C:3KQ500 4.2 45.3 1.0
C12 C:3KQ500 4.4 43.9 1.0
CD1 C:ILE336 4.4 32.2 1.0
NE2 C:HIS160 4.4 34.4 1.0
O C:HOH629 4.4 22.1 1.0
C3 C:3KQ500 4.6 45.3 1.0
O C:HOH616 4.7 36.5 1.0
C31 C:3KQ500 4.7 53.2 1.0
CE2 C:PHE340 4.8 32.9 1.0
O22 C:3KQ500 4.8 46.0 1.0

Chlorine binding site 6 out of 8 in 4wcu

Go back to Chlorine Binding Sites List in 4wcu
Chlorine binding site 6 out of 8 in the PDE4 Complexed with Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of PDE4 Complexed with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl500

b:45.9
occ:1.00
 CL8 C:3KQ500 0.0 45.9 1.0
C2 C:3KQ500 1.8 45.3 1.0
C3 C:3KQ500 2.8 45.3 1.0
C1 C:3KQ500 2.8 44.7 1.0
C9 C:3KQ500 3.1 44.2 1.0
OD2 C:ASP318 3.2 35.0 1.0
CD2 C:LEU319 3.5 35.8 1.0
CG C:ASP318 3.5 36.6 1.0
OD1 C:ASP318 3.8 34.5 1.0
O C:HOH634 3.8 28.8 1.0
C10 C:3KQ500 4.0 44.5 1.0
N4 C:3KQ500 4.0 45.4 1.0
C6 C:3KQ500 4.2 44.5 1.0
O11 C:3KQ500 4.2 43.8 1.0
CB C:ASP318 4.4 36.9 1.0
CG C:LEU319 4.4 36.2 1.0
SD C:MET273 4.6 56.2 1.0
C5 C:3KQ500 4.6 45.4 1.0
O C:ASP318 4.6 36.8 1.0
O C:THR271 4.7 44.0 1.0
ZN C:ZN501 4.7 48.1 1.0
C C:ASP318 4.8 37.5 1.0
CG C:MET273 4.8 53.5 1.0

Chlorine binding site 7 out of 8 in 4wcu

Go back to Chlorine Binding Sites List in 4wcu
Chlorine binding site 7 out of 8 in the PDE4 Complexed with Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of PDE4 Complexed with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl500

b:53.4
occ:1.00
 CL7 D:3KQ500 0.0 53.4 1.0
C6 D:3KQ500 1.8 52.6 1.0
C1 D:3KQ500 2.8 52.4 1.0
C5 D:3KQ500 2.8 52.4 1.0
C9 D:3KQ500 3.1 51.3 1.0
C10 D:3KQ500 3.6 49.3 1.0
CZ D:PHE340 3.7 40.3 1.0
CE1 D:PHE340 3.7 39.7 1.0
O11 D:3KQ500 3.8 50.4 1.0
CE1 D:HIS160 4.0 40.5 1.0
C29 D:3KQ500 4.1 58.0 1.0
N4 D:3KQ500 4.1 52.4 1.0
C30 D:3KQ500 4.1 58.1 1.0
C2 D:3KQ500 4.1 52.6 1.0
O D:HOH656 4.2 41.4 1.0
O D:HOH647 4.3 29.3 1.0
CD1 D:ILE336 4.3 47.1 1.0
NE2 D:HIS160 4.5 39.1 1.0
C12 D:3KQ500 4.5 48.7 1.0
C3 D:3KQ500 4.6 52.6 1.0
O22 D:3KQ500 4.8 48.8 1.0

Chlorine binding site 8 out of 8 in 4wcu

Go back to Chlorine Binding Sites List in 4wcu
Chlorine binding site 8 out of 8 in the PDE4 Complexed with Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of PDE4 Complexed with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl500

b:52.4
occ:1.00
 CL8 D:3KQ500 0.0 52.4 1.0
C2 D:3KQ500 1.8 52.6 1.0
C3 D:3KQ500 2.8 52.6 1.0
C1 D:3KQ500 2.8 52.4 1.0
C9 D:3KQ500 3.2 51.3 1.0
OD2 D:ASP318 3.2 42.0 1.0
CD2 D:LEU319 3.3 42.4 1.0
CG D:ASP318 3.7 41.7 1.0
C10 D:3KQ500 3.8 49.3 1.0
O11 D:3KQ500 3.9 50.4 1.0
N4 D:3KQ500 4.0 52.4 1.0
OD1 D:ASP318 4.1 40.5 1.0
C6 D:3KQ500 4.1 52.6 1.0
CB D:ASP318 4.5 42.0 1.0
CG D:MET273 4.5 51.6 1.0
CG D:LEU319 4.5 43.3 1.0
C5 D:3KQ500 4.6 52.4 1.0
SD D:MET273 4.7 53.9 1.0
O D:THR271 4.8 43.4 1.0
ZN D:ZN501 4.9 50.7 1.0
C D:ASP318 4.9 42.6 1.0
O D:ASP318 4.9 41.7 1.0
C12 D:3KQ500 4.9 48.7 1.0

Reference:

J.Felding, M.D.Sorensen, T.D.Poulsen, J.Larsen, C.Andersson, P.Refer, K.Engell, L.G.Ladefoged, T.Thormann, A.M.Vinggaard, P.Hegardt, A.Sohoel, S.F.Nielsen. Discovery and Early Clinical Development of 2-{6-[2-(3,5-Dichloro-4-Pyridyl)Acetyl]-2, 3-Dimethoxyphenoxy}-N-Propylacetamide (Leo 29102), A Soft-Drug Inhibitor of Phosphodiesterase 4 For Topical Treatment of Atopic Dermatitis. J. Med. Chem. V. 57 5893 2014.
ISSN: ISSN 0022-2623
PubMed: 24984230
DOI: 10.1021/JM500378A
Page generated: Sat Dec 12 11:17:39 2020

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