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Zinc 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:

Chlorine (Cl) 8 atoms

Zinc Binding Sites:

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

Zinc binding site 1 out of 8 in 4w1o

Go back to Zinc Binding Sites List in 4w1o
Zinc binding site 1 out of 8 in the PDE4D Complexed with Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of PDE4D Complexed with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:45.0
occ:1.00
 OD2 A:ASP201 2.1 28.3 1.0
NE2 A:HIS200 2.2 26.7 1.0
OD1 A:ASP318 2.3 27.2 1.0
NE2 A:HIS164 2.3 29.0 1.0
CG A:ASP201 3.2 26.8 1.0
CD2 A:HIS200 3.2 24.6 1.0
CE1 A:HIS164 3.2 27.1 1.0
CE1 A:HIS200 3.2 26.5 1.0
CG A:ASP318 3.2 31.4 1.0
CD2 A:HIS164 3.4 27.4 1.0
OD2 A:ASP318 3.5 32.2 1.0
OD1 A:ASP201 3.7 29.1 1.0
ZN A:ZN503 4.1 75.4 1.0
CD2 A:HIS160 4.1 23.4 1.0
ND1 A:HIS200 4.3 25.6 1.0
CG A:HIS200 4.3 26.5 1.0
CB A:ASP201 4.3 26.1 1.0
NE2 A:HIS160 4.4 24.4 1.0
ND1 A:HIS164 4.4 25.7 1.0
CG A:HIS164 4.5 26.4 1.0
CB A:ASP318 4.6 30.1 1.0
CG2 A:VAL168 4.6 23.9 1.0
CA A:ASP318 5.0 29.9 1.0

Zinc binding site 2 out of 8 in 4w1o

Go back to Zinc Binding Sites List in 4w1o
Zinc binding site 2 out of 8 in the PDE4D Complexed with Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of PDE4D Complexed with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:75.4
occ:1.00
 OD1 A:ASP201 2.3 29.1 1.0
O A:HOH743 2.3 35.5 1.0
O A:HOH744 2.4 32.4 1.0
O A:HOH742 2.6 35.3 1.0
CG A:ASP201 3.3 26.8 1.0
OD2 A:ASP201 3.7 28.3 1.0
O A:HIS200 3.9 27.5 1.0
ZN A:ZN502 4.1 45.0 1.0
OG1 A:THR271 4.1 36.5 1.0
OE2 A:GLU230 4.1 32.2 1.0
NE2 A:HIS233 4.2 23.9 1.0
CD2 A:HIS200 4.3 24.6 1.0
N4 A:3GJ501 4.3 53.4 1.0
CD2 A:HIS233 4.3 22.2 1.0
O A:HOH726 4.4 37.5 1.0
O A:THR271 4.5 37.3 1.0
C5 A:3GJ501 4.5 53.5 1.0
CB A:THR271 4.6 36.6 1.0
CB A:ASP201 4.6 26.1 1.0
CG A:GLU230 4.6 30.7 1.0
NE2 A:HIS200 4.7 26.7 1.0
OD2 A:ASP318 4.7 32.2 1.0
CD2 A:HIS204 4.8 23.8 1.0
CA A:ASP201 4.8 25.6 1.0
CD A:GLU230 4.8 31.9 1.0
C A:HIS200 4.9 26.2 1.0
C3 A:3GJ501 4.9 53.8 1.0

Zinc binding site 3 out of 8 in 4w1o

Go back to Zinc Binding Sites List in 4w1o
Zinc binding site 3 out of 8 in the PDE4D Complexed with Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of PDE4D Complexed with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:46.7
occ:1.00
 OD2 B:ASP201 2.2 27.8 1.0
NE2 B:HIS164 2.2 23.7 1.0
OD1 B:ASP318 2.3 34.8 1.0
NE2 B:HIS200 2.4 30.3 1.0
CD2 B:HIS200 3.1 28.4 1.0
CD2 B:HIS164 3.2 24.9 1.0
CG B:ASP318 3.2 32.6 1.0
CE1 B:HIS164 3.2 24.8 1.0
CG B:ASP201 3.3 28.1 1.0
OD2 B:ASP318 3.4 34.1 1.0
CE1 B:HIS200 3.5 31.4 1.0
OD1 B:ASP201 3.9 29.8 1.0
ZN B:ZN503 4.0 82.8 1.0
CD2 B:HIS160 4.1 21.1 1.0
O B:HOH640 4.3 32.5 1.0
CG B:HIS200 4.3 29.6 1.0
ND1 B:HIS164 4.3 25.6 1.0
CG B:HIS164 4.3 25.5 1.0
CB B:ASP201 4.4 27.7 1.0
NE2 B:HIS160 4.5 22.1 1.0
ND1 B:HIS200 4.5 32.0 1.0
CB B:ASP318 4.6 31.5 1.0
CG2 B:VAL168 4.6 28.5 1.0
CA B:ASP318 5.0 31.7 1.0

Zinc binding site 4 out of 8 in 4w1o

Go back to Zinc Binding Sites List in 4w1o
Zinc binding site 4 out of 8 in the PDE4D Complexed with Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of PDE4D Complexed with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn503

b:82.8
occ:1.00
 OD1 B:ASP201 2.2 29.8 1.0
O B:HOH719 2.4 28.2 1.0
O B:HOH721 2.5 42.2 1.0
O B:HOH720 2.5 27.1 1.0
CG B:ASP201 3.1 28.1 1.0
OD2 B:ASP201 3.4 27.8 1.0
O B:HIS200 4.0 27.8 1.0
ZN B:ZN502 4.0 46.7 1.0
N4 B:3GJ501 4.1 55.7 1.0
O B:HOH628 4.1 32.6 1.0
NE2 B:HIS233 4.1 27.3 1.0
OE2 B:GLU230 4.1 33.9 1.0
OG1 B:THR271 4.2 35.4 1.0
CD2 B:HIS233 4.3 28.0 1.0
C5 B:3GJ501 4.4 55.1 1.0
CD2 B:HIS204 4.4 22.7 1.0
CB B:ASP201 4.5 27.7 1.0
CD2 B:HIS200 4.5 28.4 1.0
C3 B:3GJ501 4.6 55.4 1.0
O B:HOH712 4.6 44.3 1.0
O B:THR271 4.7 37.8 1.0
NE2 B:HIS204 4.7 25.7 1.0
OD2 B:ASP318 4.8 34.1 1.0
NE2 B:HIS160 4.8 22.1 1.0
CD2 B:HIS160 4.8 21.1 1.0
CA B:ASP201 4.8 27.5 1.0
CB B:THR271 4.9 37.2 1.0
C B:HIS200 4.9 28.0 1.0
CG B:GLU230 4.9 29.8 1.0
CD B:GLU230 5.0 32.5 1.0

Zinc binding site 5 out of 8 in 4w1o

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Zinc binding site 5 out of 8 in the PDE4D Complexed with Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of PDE4D Complexed with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn502

b:49.4
occ:1.00
 NE2 C:HIS200 2.2 34.3 1.0
NE2 C:HIS164 2.3 33.9 1.0
OD1 C:ASP318 2.3 39.2 1.0
OD2 C:ASP201 2.4 33.5 1.0
CD2 C:HIS200 3.1 31.6 1.0
CD2 C:HIS164 3.2 32.2 1.0
CG C:ASP318 3.3 40.7 1.0
CE1 C:HIS200 3.3 32.6 1.0
CE1 C:HIS164 3.3 31.9 1.0
CG C:ASP201 3.3 30.9 1.0
OD2 C:ASP318 3.5 41.3 1.0
OD1 C:ASP201 3.8 30.1 1.0
ZN C:ZN503 3.9 78.2 1.0
CD2 C:HIS160 4.0 27.8 1.0
O C:HOH698 4.1 36.9 1.0
CG C:HIS200 4.2 30.5 1.0
O C:HOH688 4.2 36.3 1.0
NE2 C:HIS160 4.3 29.2 1.0
ND1 C:HIS200 4.3 31.3 1.0
ND1 C:HIS164 4.4 32.5 1.0
CG C:HIS164 4.4 32.7 1.0
CB C:ASP201 4.5 29.1 1.0
CB C:ASP318 4.6 40.7 1.0
CG2 C:VAL168 4.7 32.7 1.0
O C:HOH701 4.9 36.9 1.0

Zinc binding site 6 out of 8 in 4w1o

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Zinc binding site 6 out of 8 in the PDE4D Complexed with Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of PDE4D Complexed with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn503

b:78.2
occ:1.00
 O C:HOH698 2.2 36.9 1.0
O C:HOH700 2.4 36.3 1.0
OD1 C:ASP201 2.4 30.1 1.0
O C:HOH701 2.5 36.9 1.0
O C:HOH699 2.5 46.1 1.0
CG C:ASP201 3.4 30.9 1.0
OD2 C:ASP201 3.6 33.5 1.0
ZN C:ZN502 3.9 49.4 1.0
N4 C:3GJ501 4.1 62.9 1.0
O C:HOH636 4.1 42.6 1.0
OE2 C:GLU230 4.2 35.4 1.0
O C:HIS200 4.2 28.4 1.0
OG1 C:THR271 4.3 42.0 1.0
NE2 C:HIS233 4.4 23.6 1.0
C5 C:3GJ501 4.4 63.0 1.0
CD2 C:HIS200 4.4 31.6 1.0
CD2 C:HIS233 4.5 23.3 1.0
C3 C:3GJ501 4.6 63.7 1.0
O C:THR271 4.6 44.5 1.0
CD2 C:HIS204 4.6 24.0 1.0
CB C:ASP201 4.7 29.1 1.0
NE2 C:HIS160 4.7 29.2 1.0
CD2 C:HIS160 4.8 27.8 1.0
OD2 C:ASP318 4.8 41.3 1.0
NE2 C:HIS200 4.8 34.3 1.0
NE2 C:HIS204 4.9 25.3 1.0
CB C:THR271 5.0 42.9 1.0
CD C:GLU230 5.0 34.2 1.0
CG C:GLU230 5.0 30.6 1.0

Zinc binding site 7 out of 8 in 4w1o

Go back to Zinc Binding Sites List in 4w1o
Zinc binding site 7 out of 8 in the PDE4D Complexed with Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of PDE4D Complexed with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn502

b:50.9
occ:1.00
 OD2 D:ASP201 2.2 32.7 1.0
NE2 D:HIS164 2.3 31.8 1.0
OD1 D:ASP318 2.3 38.7 1.0
NE2 D:HIS200 2.5 30.1 1.0
CE1 D:HIS164 3.1 29.0 1.0
CG D:ASP201 3.2 29.8 1.0
CD2 D:HIS200 3.2 30.2 1.0
CG D:ASP318 3.3 39.4 1.0
CD2 D:HIS164 3.4 32.2 1.0
CE1 D:HIS200 3.6 32.5 1.0
OD1 D:ASP201 3.6 31.3 1.0
OD2 D:ASP318 3.6 40.2 1.0
ZN D:ZN503 4.0 87.0 1.0
CD2 D:HIS160 4.2 29.7 1.0
O D:HOH701 4.3 36.4 1.0
ND1 D:HIS164 4.3 32.4 1.0
CB D:ASP201 4.4 30.1 1.0
CG D:HIS200 4.4 31.3 1.0
O D:HOH692 4.4 31.8 1.0
NE2 D:HIS160 4.4 28.4 1.0
CG D:HIS164 4.5 33.3 1.0
ND1 D:HIS200 4.6 31.4 1.0
CB D:ASP318 4.6 39.2 1.0
CG2 D:VAL168 4.8 37.7 1.0
O D:HOH703 4.9 34.1 1.0

Zinc binding site 8 out of 8 in 4w1o

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Zinc binding site 8 out of 8 in the PDE4D Complexed with Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of PDE4D Complexed with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn503

b:87.0
occ:1.00
 OD1 D:ASP201 2.3 31.3 1.0
O D:HOH701 2.3 36.4 1.0
O D:HOH703 2.4 34.1 1.0
O D:HOH702 2.4 33.9 1.0
CG D:ASP201 3.3 29.8 1.0
OD2 D:ASP201 3.7 32.7 1.0
NE2 D:HIS233 3.9 26.5 1.0
ZN D:ZN502 4.0 50.9 1.0
O D:HIS200 4.0 30.9 1.0
O D:HOH639 4.1 36.5 1.0
CD2 D:HIS233 4.1 27.4 1.0
OE2 D:GLU230 4.1 35.7 1.0
CD2 D:HIS204 4.4 26.5 1.0
OG1 D:THR271 4.5 43.6 1.0
N4 D:3GJ501 4.5 63.4 1.0
CD2 D:HIS200 4.6 30.2 1.0
CB D:ASP201 4.6 30.1 1.0
NE2 D:HIS204 4.6 26.3 1.0
C5 D:3GJ501 4.7 63.3 1.0
CA D:ASP201 4.8 30.3 1.0
O D:HOH693 4.8 57.2 1.0
CG D:GLU230 4.8 31.9 1.0
CD2 D:HIS160 4.9 29.7 1.0
CD D:GLU230 4.9 32.9 1.0
C D:HIS200 4.9 31.0 1.0
NE2 D:HIS160 4.9 28.4 1.0
O D:THR271 4.9 44.5 1.0
CE1 D:HIS233 5.0 26.0 1.0
C3 D:3GJ501 5.0 63.5 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: Sun Oct 27 09:37:24 2024

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