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Magnesium in PDB 4d08: PDE2A Catalytic Domain in Complex with A Brain Penetrant Inhibitor

Enzymatic activity of PDE2A Catalytic Domain in Complex with A Brain Penetrant Inhibitor

All present enzymatic activity of PDE2A Catalytic Domain in Complex with A Brain Penetrant Inhibitor:
3.1.4.17;

Protein crystallography data

The structure of PDE2A Catalytic Domain in Complex with A Brain Penetrant Inhibitor, PDB code: 4d08 was solved by P.Buijnsters, J.I.Andres, M.Deangelis, X.Langlois, F.Rombouts, W.Sanderson, G.Tresadern, A.Trabanco, G.Vanhoof, Y.Vanroosbroeck, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.34 / 1.90
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 56.040, 74.150, 92.770, 109.04, 91.73, 91.34
R / Rfree (%) 21.289 / 24.714

Other elements in 4d08:

The structure of PDE2A Catalytic Domain in Complex with A Brain Penetrant Inhibitor also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the PDE2A Catalytic Domain in Complex with A Brain Penetrant Inhibitor (pdb code 4d08). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the PDE2A Catalytic Domain in Complex with A Brain Penetrant Inhibitor, PDB code: 4d08:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4d08

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Magnesium binding site 1 out of 4 in the PDE2A Catalytic Domain in Complex with A Brain Penetrant Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of PDE2A Catalytic Domain in Complex with A Brain Penetrant Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1919

b:12.1
occ:1.00
 OD1 A:ASP697 2.2 11.1 1.0
O A:HOH2095 2.2 12.4 1.0
O A:HOH2075 2.2 11.5 1.0
O A:HOH2077 2.2 11.4 1.0
O A:HOH2063 2.2 11.6 1.0
O A:HOH2076 2.2 12.9 1.0
CG A:ASP697 3.2 11.3 1.0
OD2 A:ASP697 3.4 12.0 1.0
ZN A:ZN1001 3.9 13.9 1.0
O A:HOH2062 4.0 14.5 1.0
O A:HOH2079 4.1 12.0 1.0
OE2 A:GLU727 4.1 14.7 1.0
NE2 A:HIS730 4.1 11.2 1.0
CD2 A:HIS696 4.2 12.2 1.0
OG1 A:THR768 4.2 13.9 1.0
O28 A:Q2T1918 4.3 18.2 1.0
O A:HIS696 4.3 10.8 1.0
CD2 A:HIS730 4.3 11.4 1.0
CB A:THR768 4.4 13.9 1.0
OD2 A:ASP808 4.5 14.8 1.0
CD2 A:HIS700 4.5 13.5 1.0
O A:THR768 4.5 13.9 1.0
CB A:ASP697 4.5 11.2 1.0
NE2 A:HIS656 4.6 14.6 1.0
NE2 A:HIS696 4.6 12.5 1.0
NE2 A:HIS700 4.6 13.5 1.0
C25 A:Q2T1918 4.7 17.9 1.0
CD2 A:HIS656 4.7 14.3 1.0
CA A:ASP697 4.9 11.1 1.0
C26 A:Q2T1918 4.9 18.2 1.0
CG A:GLU727 4.9 14.1 1.0
CD A:GLU727 5.0 14.4 1.0

Magnesium binding site 2 out of 4 in 4d08

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Magnesium binding site 2 out of 4 in the PDE2A Catalytic Domain in Complex with A Brain Penetrant Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of PDE2A Catalytic Domain in Complex with A Brain Penetrant Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1918

b:12.2
occ:1.00
 O B:HOH2048 2.2 12.0 1.0
OD1 B:ASP697 2.2 11.8 1.0
O B:HOH2060 2.2 11.9 1.0
O B:HOH2076 2.2 11.3 1.0
O B:HOH2061 2.2 12.3 1.0
O B:HOH2062 2.2 12.7 1.0
CG B:ASP697 3.1 12.0 1.0
OD2 B:ASP697 3.3 12.3 1.0
ZN B:ZN1001 3.8 13.2 1.0
O B:HOH2049 4.0 12.8 1.0
OG1 B:THR768 4.1 13.6 1.0
CD2 B:HIS696 4.1 13.0 1.0
NE2 B:HIS730 4.1 13.7 1.0
O B:HOH2064 4.2 15.8 1.0
O28 B:Q2T1917 4.2 15.7 1.0
OE2 B:GLU727 4.2 17.1 1.0
O B:HIS696 4.3 12.7 1.0
CD2 B:HIS730 4.3 13.8 1.0
NE2 B:HIS696 4.5 13.1 1.0
CB B:ASP697 4.5 12.0 1.0
CB B:THR768 4.5 13.5 1.0
NE2 B:HIS656 4.5 14.6 1.0
OD2 B:ASP808 4.5 14.1 1.0
CD2 B:HIS700 4.6 16.3 1.0
O B:THR768 4.7 14.0 1.0
CD2 B:HIS656 4.7 14.5 1.0
C25 B:Q2T1917 4.8 16.5 1.0
NE2 B:HIS700 4.8 16.3 1.0
C29 B:Q2T1917 4.8 15.3 1.0
CA B:ASP697 4.8 12.3 1.0
C26 B:Q2T1917 4.8 16.4 1.0

Magnesium binding site 3 out of 4 in 4d08

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Magnesium binding site 3 out of 4 in the PDE2A Catalytic Domain in Complex with A Brain Penetrant Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of PDE2A Catalytic Domain in Complex with A Brain Penetrant Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1918

b:11.6
occ:1.00
 OD1 C:ASP697 2.2 12.2 1.0
O C:HOH2037 2.2 11.9 1.0
O C:HOH2061 2.2 10.9 1.0
O C:HOH2031 2.2 11.0 1.0
O C:HOH2039 2.2 11.3 1.0
O C:HOH2038 2.2 12.3 1.0
CG C:ASP697 3.1 13.1 1.0
OD2 C:ASP697 3.4 13.3 1.0
ZN C:ZN1001 3.8 14.2 1.0
O C:HOH2032 3.9 13.7 1.0
OE2 C:GLU727 4.1 16.2 1.0
CD2 C:HIS696 4.1 14.0 1.0
NE2 C:HIS730 4.1 11.9 1.0
OG1 C:THR768 4.1 14.3 1.0
O C:HOH2041 4.2 10.6 1.0
O28 C:Q2T1917 4.2 15.8 1.0
O C:HIS696 4.3 13.6 1.0
CD2 C:HIS730 4.4 11.9 1.0
OD2 C:ASP808 4.4 14.7 1.0
O C:THR768 4.5 14.6 1.0
NE2 C:HIS656 4.5 14.6 1.0
CD2 C:HIS700 4.5 14.9 1.0
CB C:ASP697 4.5 13.0 1.0
CB C:THR768 4.5 14.3 1.0
NE2 C:HIS696 4.5 14.1 1.0
CD2 C:HIS656 4.6 14.4 1.0
O C:HOH2048 4.7 22.0 1.0
NE2 C:HIS700 4.7 14.8 1.0
C29 C:Q2T1917 4.8 16.2 1.0
CA C:ASP697 4.8 13.2 1.0
C25 C:Q2T1917 4.8 16.2 1.0
C26 C:Q2T1917 4.9 16.2 1.0
CD C:GLU727 4.9 15.9 1.0
CG C:GLU727 4.9 15.4 1.0

Magnesium binding site 4 out of 4 in 4d08

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Magnesium binding site 4 out of 4 in the PDE2A Catalytic Domain in Complex with A Brain Penetrant Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of PDE2A Catalytic Domain in Complex with A Brain Penetrant Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1923

b:11.8
occ:1.00
 O D:HOH2041 2.2 12.4 1.0
OD1 D:ASP697 2.2 11.8 1.0
O D:HOH2030 2.2 11.2 1.0
O D:HOH2043 2.2 11.1 1.0
O D:HOH2066 2.2 11.8 1.0
O D:HOH2042 2.2 12.2 1.0
CG D:ASP697 3.1 12.3 1.0
OD2 D:ASP697 3.4 12.4 1.0
ZN D:ZN1001 3.8 13.3 1.0
O D:HOH2031 3.9 13.6 1.0
OE2 D:GLU727 4.0 13.4 1.0
CD2 D:HIS696 4.1 12.8 1.0
NE2 D:HIS730 4.2 11.6 1.0
O D:HOH2045 4.2 13.9 1.0
OG1 D:THR768 4.2 12.6 1.0
O28 D:Q2T1922 4.3 15.8 1.0
O D:HIS696 4.3 12.4 1.0
CD2 D:HIS730 4.4 11.8 1.0
CD2 D:HIS700 4.4 15.3 1.0
OD2 D:ASP808 4.4 13.3 1.0
CB D:THR768 4.5 12.7 1.0
O D:THR768 4.5 12.8 1.0
CB D:ASP697 4.5 12.3 1.0
NE2 D:HIS696 4.5 12.9 1.0
NE2 D:HIS700 4.6 15.3 1.0
NE2 D:HIS656 4.7 14.6 1.0
CD2 D:HIS656 4.8 14.5 1.0
C25 D:Q2T1922 4.8 16.0 1.0
CA D:ASP697 4.8 12.5 1.0
CD D:GLU727 4.9 13.3 1.0
O D:HOH2053 4.9 25.0 1.0
C26 D:Q2T1922 4.9 15.8 1.0
CG D:GLU727 5.0 13.0 1.0
C29 D:Q2T1922 5.0 15.7 1.0
O D:HOH2083 5.0 19.7 1.0

Reference:

P.Buijnsters, M.De Angelis, X.Langlois, F.J.R.Rombouts, W.Sanderson, G.Tresadern, A.Ritchie, A.A.Trabanco, G.Vanhoof, Y.V.Roosbroeck, J.Andres. Structure-Based Design of A Potent, Selective, and Brain Penetrating PDE2 Inhibitor with Demonstrated Target Engagement. Acs Med.Chem.Lett. V. 5 1049 2014.
ISSN: ISSN 1948-5875
PubMed: 25221665
DOI: 10.1021/ML500262U
Page generated: Mon Aug 11 07:22:46 2025

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