Atomistry » Chlorine » PDB 4wcu-4wki » 4wcu
Atomistry »
  Chlorine »
    PDB 4wcu-4wki »
      4wcu »

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: Fri Jul 26 02:51:33 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy