Atomistry » Zinc » PDB 4uyo-4w8y » 4w1o
Atomistry »
  Zinc »
    PDB 4uyo-4w8y »
      4w1o »

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

Go back to Zinc Binding Sites List in 4w1o
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

Go back to Zinc Binding Sites List in 4w1o
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

Go back to Zinc Binding Sites List in 4w1o
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: Wed Aug 20 22:55:43 2025

Last articles

Zn in 5LQQ
Zn in 5LMX
Zn in 5LPT
Zn in 5LPQ
Zn in 5LPS
Zn in 5LPP
Zn in 5LPO
Zn in 5LPE
Zn in 5LNK
Zn in 5LOS
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy