Atomistry » Chlorine » PDB 4v35-4wcc » 4w1o
Atomistry »
  Chlorine »
    PDB 4v35-4wcc »
      4w1o »

Chlorine in PDB 4w1o: PDE4D Complexed with Inhibitor

Enzymatic activity of PDE4D Complexed with Inhibitor

All present enzymatic activity of PDE4D Complexed with Inhibitor:
3.1.4.53;

Protein crystallography data

The structure of PDE4D Complexed with Inhibitor, PDB code: 4w1o 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) 92.45 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 99.426, 112.671, 161.077, 90.00, 90.00, 90.00
R / Rfree (%) 23.7 / 28.1

Other elements in 4w1o:

The structure of PDE4D Complexed with Inhibitor also contains other interesting chemical elements:

Zinc (Zn) 8 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the PDE4D Complexed with Inhibitor (pdb code 4w1o). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the PDE4D Complexed with Inhibitor, PDB code: 4w1o:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 4w1o

Go back to Chlorine Binding Sites List in 4w1o
Chlorine binding site 1 out of 8 in the PDE4D 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 PDE4D Complexed with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl501

b:53.5
occ:1.00
 CL7 A:3GJ501 0.0 53.5 1.0
C6 A:3GJ501 1.8 53.0 1.0
C5 A:3GJ501 2.8 53.5 1.0
C1 A:3GJ501 2.8 53.9 1.0
N9 A:3GJ501 3.1 54.1 1.0
OD2 A:ASP318 3.2 32.2 1.0
CD2 A:LEU319 3.2 32.1 1.0
CG A:ASP318 3.5 31.4 1.0
CG A:LEU319 3.7 30.9 1.0
O A:ASP318 3.8 29.5 1.0
C10 A:3GJ501 3.9 54.3 1.0
O A:HOH730 3.9 29.4 1.0
OD1 A:ASP318 4.0 27.2 1.0
N4 A:3GJ501 4.0 53.4 1.0
CB A:ASP318 4.1 30.1 1.0
C A:ASP318 4.1 30.0 1.0
C2 A:3GJ501 4.1 53.7 1.0
O11 A:3GJ501 4.3 54.3 1.0
SD A:MET273 4.3 42.5 1.0
N A:LEU319 4.6 29.8 1.0
C3 A:3GJ501 4.6 53.8 1.0
CD1 A:LEU319 4.7 31.1 1.0
CG A:MET273 4.7 40.5 1.0
CA A:ASP318 4.7 29.9 1.0
CA A:LEU319 4.7 29.9 1.0
CB A:LEU319 4.8 29.9 1.0
C12 A:3GJ501 4.8 54.3 1.0
C13 A:3GJ501 5.0 54.1 1.0

Chlorine binding site 2 out of 8 in 4w1o

Go back to Chlorine Binding Sites List in 4w1o
Chlorine binding site 2 out of 8 in the PDE4D 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 PDE4D Complexed with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl501

b:54.4
occ:1.00
 CL8 A:3GJ501 0.0 54.4 1.0
C2 A:3GJ501 1.8 53.7 1.0
C3 A:3GJ501 2.8 53.8 1.0
C1 A:3GJ501 2.8 53.9 1.0
N9 A:3GJ501 3.1 54.1 1.0
O A:HOH658 3.3 47.8 1.0
O11 A:3GJ501 3.4 54.3 1.0
C10 A:3GJ501 3.4 54.3 1.0
CE1 A:HIS160 3.6 24.4 1.0
CZ A:PHE340 3.8 39.3 1.0
CE1 A:PHE340 3.9 38.4 1.0
NE2 A:HIS160 4.0 24.4 1.0
N4 A:3GJ501 4.1 53.4 1.0
CD1 A:ILE336 4.1 34.0 1.0
O A:HOH728 4.1 48.4 1.0
C6 A:3GJ501 4.1 53.0 1.0
O A:HOH726 4.3 37.5 1.0
C12 A:3GJ501 4.4 54.3 1.0
O A:HOH729 4.5 36.2 1.0
C5 A:3GJ501 4.6 53.5 1.0
O A:HOH740 4.7 48.5 1.0
ND1 A:HIS160 4.8 25.5 1.0
CG1 A:ILE336 5.0 34.3 1.0

Chlorine binding site 3 out of 8 in 4w1o

Go back to Chlorine Binding Sites List in 4w1o
Chlorine binding site 3 out of 8 in the PDE4D 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 PDE4D Complexed with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl501

b:55.9
occ:1.00
 CL7 B:3GJ501 0.0 55.9 1.0
C6 B:3GJ501 1.8 54.5 1.0
C5 B:3GJ501 2.7 55.1 1.0
C1 B:3GJ501 2.8 56.2 1.0
CD2 B:LEU319 3.1 35.3 1.0
N9 B:3GJ501 3.1 56.3 1.0
O B:HOH640 3.3 32.5 1.0
OD2 B:ASP318 3.3 34.1 1.0
CG B:ASP318 3.5 32.6 1.0
CG B:LEU319 3.7 32.7 1.0
O B:ASP318 3.7 31.5 1.0
O B:HOH713 3.8 35.2 1.0
OD1 B:ASP318 4.0 34.8 1.0
N4 B:3GJ501 4.0 55.7 1.0
C10 B:3GJ501 4.0 56.9 1.0
C B:ASP318 4.1 31.8 1.0
CB B:ASP318 4.1 31.5 1.0
C2 B:3GJ501 4.2 55.4 1.0
SD B:MET273 4.2 46.1 1.0
O11 B:3GJ501 4.5 56.1 1.0
N B:LEU319 4.6 32.2 1.0
C3 B:3GJ501 4.6 55.4 1.0
CD1 B:LEU319 4.7 34.6 1.0
CA B:ASP318 4.7 31.7 1.0
CA B:LEU319 4.8 32.6 1.0
CG B:MET273 4.8 42.6 1.0
CB B:LEU319 4.8 32.2 1.0
C12 B:3GJ501 4.9 57.3 1.0

Chlorine binding site 4 out of 8 in 4w1o

Go back to Chlorine Binding Sites List in 4w1o
Chlorine binding site 4 out of 8 in the PDE4D 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 PDE4D Complexed with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl501

b:55.7
occ:1.00
 CL8 B:3GJ501 0.0 55.7 1.0
C2 B:3GJ501 1.8 55.4 1.0
C3 B:3GJ501 2.8 55.4 1.0
C1 B:3GJ501 2.9 56.2 1.0
O B:HOH711 3.0 50.1 1.0
N9 B:3GJ501 3.2 56.3 1.0
O11 B:3GJ501 3.4 56.1 1.0
C10 B:3GJ501 3.4 56.9 1.0
CE1 B:HIS160 3.6 21.6 1.0
NE2 B:HIS160 3.9 22.1 1.0
CZ B:PHE340 3.9 33.0 1.0
CE1 B:PHE340 4.0 34.3 1.0
N4 B:3GJ501 4.0 55.7 1.0
O B:HOH628 4.1 32.6 1.0
O B:HOH714 4.1 50.4 1.0
O B:HOH702 4.1 35.7 1.0
C6 B:3GJ501 4.2 54.5 1.0
O B:HOH715 4.2 59.6 1.0
CD1 B:ILE336 4.3 32.8 1.0
O B:HOH647 4.4 46.2 1.0
C12 B:3GJ501 4.5 57.3 1.0
C5 B:3GJ501 4.6 55.1 1.0
ND1 B:HIS160 4.8 23.3 1.0

Chlorine binding site 5 out of 8 in 4w1o

Go back to Chlorine Binding Sites List in 4w1o
Chlorine binding site 5 out of 8 in the PDE4D 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 PDE4D Complexed with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl501

b:64.1
occ:1.00
 CL7 C:3GJ501 0.0 64.1 1.0
C6 C:3GJ501 1.8 63.0 1.0
C5 C:3GJ501 2.8 63.0 1.0
C1 C:3GJ501 2.8 62.9 1.0
N9 C:3GJ501 3.1 61.5 1.0
CD2 C:LEU319 3.3 38.3 1.0
O C:HOH688 3.3 36.3 1.0
OD2 C:ASP318 3.5 41.3 1.0
CG C:LEU319 3.6 39.6 1.0
CG C:ASP318 3.6 40.7 1.0
O C:ASP318 3.8 40.4 1.0
O C:HOH687 3.9 32.2 1.0
C10 C:3GJ501 4.0 59.6 1.0
OD1 C:ASP318 4.0 39.2 1.0
N4 C:3GJ501 4.0 62.9 1.0
C C:ASP318 4.1 40.4 1.0
CB C:ASP318 4.1 40.7 1.0
C2 C:3GJ501 4.2 63.3 1.0
O11 C:3GJ501 4.4 59.6 1.0
SD C:MET273 4.4 49.0 1.0
N C:LEU319 4.5 40.4 1.0
CD1 C:LEU319 4.6 37.3 1.0
C3 C:3GJ501 4.6 63.7 1.0
CB C:LEU319 4.7 39.8 1.0
CA C:LEU319 4.7 40.6 1.0
CG C:MET273 4.7 47.5 1.0
CA C:ASP318 4.7 40.1 1.0
C12 C:3GJ501 4.9 59.3 1.0

Chlorine binding site 6 out of 8 in 4w1o

Go back to Chlorine Binding Sites List in 4w1o
Chlorine binding site 6 out of 8 in the PDE4D 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 PDE4D Complexed with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl501

b:63.3
occ:1.00
 CL8 C:3GJ501 0.0 63.3 1.0
C2 C:3GJ501 1.8 63.3 1.0
C3 C:3GJ501 2.8 63.7 1.0
C1 C:3GJ501 2.8 62.9 1.0
N9 C:3GJ501 3.1 61.5 1.0
O11 C:3GJ501 3.3 59.6 1.0
C10 C:3GJ501 3.3 59.6 1.0
O C:HOH702 3.4 54.3 1.0
CE1 C:HIS160 3.5 27.2 1.0
CZ C:PHE340 3.8 36.2 1.0
O C:HOH651 3.9 37.7 1.0
CE1 C:PHE340 3.9 37.9 1.0
NE2 C:HIS160 3.9 29.2 1.0
CD1 C:ILE336 4.0 39.2 1.0
N4 C:3GJ501 4.1 62.9 1.0
O C:HOH636 4.1 42.6 1.0
C6 C:3GJ501 4.2 63.0 1.0
O C:HOH631 4.3 36.1 1.0
C12 C:3GJ501 4.4 59.3 1.0
O C:HOH698 4.4 36.9 1.0
C5 C:3GJ501 4.6 63.0 1.0
ND1 C:HIS160 4.8 27.9 1.0
CG1 C:ILE336 5.0 39.3 1.0

Chlorine binding site 7 out of 8 in 4w1o

Go back to Chlorine Binding Sites List in 4w1o
Chlorine binding site 7 out of 8 in the PDE4D 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 PDE4D Complexed with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl501

b:64.1
occ:1.00
 CL7 D:3GJ501 0.0 64.1 1.0
C6 D:3GJ501 1.8 63.4 1.0
C5 D:3GJ501 2.8 63.3 1.0
C1 D:3GJ501 2.8 63.7 1.0
OD2 D:ASP318 2.9 40.2 1.0
N9 D:3GJ501 3.1 62.9 1.0
CD2 D:LEU319 3.4 40.8 1.0
O D:HOH692 3.5 31.8 1.0
O D:HOH698 3.6 36.9 1.0
CG D:ASP318 3.6 39.4 1.0
CG D:LEU319 3.9 40.0 1.0
C10 D:3GJ501 4.0 61.7 1.0
N4 D:3GJ501 4.0 63.4 1.0
OD1 D:ASP318 4.1 38.7 1.0
C2 D:3GJ501 4.2 63.5 1.0
O D:ASP318 4.3 39.7 1.0
CB D:ASP318 4.4 39.2 1.0
O11 D:3GJ501 4.4 60.5 1.0
C D:ASP318 4.4 39.6 1.0
SD D:MET273 4.5 49.8 1.0
C3 D:3GJ501 4.6 63.5 1.0
N D:LEU319 4.7 39.3 1.0
CG D:MET273 4.7 47.7 1.0
CD1 D:LEU319 4.9 41.1 1.0
CA D:LEU319 4.9 39.3 1.0
CB D:LEU319 4.9 39.4 1.0
C12 D:3GJ501 5.0 61.6 1.0

Chlorine binding site 8 out of 8 in 4w1o

Go back to Chlorine Binding Sites List in 4w1o
Chlorine binding site 8 out of 8 in the PDE4D 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 PDE4D Complexed with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl501

b:63.4
occ:1.00
 CL8 D:3GJ501 0.0 63.4 1.0
C2 D:3GJ501 1.8 63.5 1.0
C3 D:3GJ501 2.8 63.5 1.0
C1 D:3GJ501 2.8 63.7 1.0
N9 D:3GJ501 3.1 62.9 1.0
O D:HOH660 3.1 53.9 1.0
O11 D:3GJ501 3.2 60.5 1.0
C10 D:3GJ501 3.3 61.7 1.0
CE1 D:HIS160 3.7 28.7 1.0
O D:HOH700 3.8 41.3 1.0
CZ D:PHE340 3.9 34.5 1.0
CE1 D:PHE340 4.0 34.2 1.0
NE2 D:HIS160 4.1 28.4 1.0
N4 D:3GJ501 4.1 63.4 1.0
C6 D:3GJ501 4.2 63.4 1.0
O D:HOH639 4.2 36.5 1.0
CD1 D:ILE336 4.2 33.3 1.0
C12 D:3GJ501 4.3 61.6 1.0
O D:HOH644 4.5 39.2 1.0
O D:HOH701 4.5 36.4 1.0
C5 D:3GJ501 4.6 63.3 1.0
ND1 D:HIS160 4.9 30.4 1.0
C17 D:3GJ501 5.0 62.5 1.0

Reference:

J.Felding, M.D.Sorensen, T.D.Poulsen, J.Larsen, C.Andersson, P.Refer, K.Engell, L.G.Ladgefoged, T.Thormann, A.M.Vinggaard, P.Hegardt, A.Sohoel, S.F.Nielse. 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 11:17:04 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy