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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

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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

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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

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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

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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: Fri Jul 26 02:41:14 2024

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