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Magnesium in PDB 4d09: 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: 4d09 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) 19.77 / 2.50
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 56.140, 73.430, 91.620, 109.37, 91.82, 91.05
R / Rfree (%) 20.642 / 27.746

Other elements in 4d09:

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 4d09). 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: 4d09:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4d09

Go back to Magnesium Binding Sites List in 4d09
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:Mg1002

b:11.5
occ:1.00
 O A:HOH2043 2.0 9.4 1.0
OD1 A:ASP697 2.1 14.3 1.0
O A:HOH2042 2.1 25.5 1.0
O A:HOH2034 2.2 17.0 1.0
O A:HOH2054 2.3 9.8 1.0
O A:HOH2044 2.3 7.1 1.0
CG A:ASP697 3.1 15.3 1.0
OD2 A:ASP697 3.4 15.4 1.0
NE2 A:HIS730 3.9 19.3 1.0
ZN A:ZN1001 3.9 26.5 1.0
CD2 A:HIS730 4.0 19.0 1.0
OE2 A:GLU727 4.1 19.3 1.0
OG1 A:THR768 4.1 16.9 1.0
O A:HIS696 4.1 15.4 1.0
CD2 A:HIS696 4.2 15.7 1.0
O A:HOH2033 4.4 18.1 1.0
CB A:THR768 4.4 17.8 1.0
CB A:ASP697 4.5 15.7 1.0
CD2 A:HIS700 4.5 19.6 1.0
NE2 A:HIS656 4.5 20.5 1.0
C28 A:7881 4.5 21.3 1.0
O A:THR768 4.6 18.8 1.0
NE2 A:HIS700 4.6 19.8 1.0
CD2 A:HIS656 4.6 20.3 1.0
NE2 A:HIS696 4.6 15.6 1.0
CG A:GLU727 4.7 18.7 1.0
OD2 A:ASP808 4.8 19.7 1.0
CD A:GLU727 4.8 18.9 1.0
CA A:ASP697 4.8 15.9 1.0
C27 A:7881 4.9 21.4 1.0

Magnesium binding site 2 out of 4 in 4d09

Go back to Magnesium Binding Sites List in 4d09
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:Mg1002

b:14.3
occ:1.00
 O B:HOH2045 2.1 7.3 1.0
O B:HOH2031 2.1 6.7 1.0
OD1 B:ASP697 2.2 18.6 1.0
O B:HOH2029 2.2 5.7 1.0
O B:HOH2032 2.3 13.1 1.0
CG B:ASP697 3.2 18.5 1.0
OD2 B:ASP697 3.6 18.0 1.0
OG1 B:THR768 3.7 18.0 1.0
ZN B:ZN1001 3.9 24.9 1.0
CD2 B:HIS696 3.9 20.7 1.0
OE2 B:GLU727 4.0 20.5 1.0
O B:HIS696 4.1 21.4 1.0
NE2 B:HIS730 4.1 18.7 1.0
CD2 B:HIS730 4.1 19.1 1.0
CB B:THR768 4.3 18.6 1.0
NE2 B:HIS696 4.3 20.8 1.0
O B:THR768 4.4 20.7 1.0
CD2 B:HIS700 4.5 22.1 1.0
NE2 B:HIS700 4.5 22.4 1.0
CB B:ASP697 4.5 18.6 1.0
OD2 B:ASP808 4.7 22.9 1.0
CG B:GLU727 4.7 20.7 1.0
CA B:ASP697 4.7 18.8 1.0
O B:HOH2034 4.8 11.7 1.0
C28 B:7881 4.8 25.1 1.0
CD B:GLU727 4.8 20.8 1.0
C B:HIS696 4.9 19.9 1.0
C B:THR768 4.9 20.2 1.0

Magnesium binding site 3 out of 4 in 4d09

Go back to Magnesium Binding Sites List in 4d09
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:Mg1002

b:28.3
occ:1.00
 O C:HOH2010 2.4 16.5 1.0
O C:HOH2009 2.8 10.4 1.0
C28 C:7881 3.1 25.0 1.0
NE2 C:HIS656 3.2 25.4 1.0
OD1 C:ASP697 3.2 21.8 1.0
NE2 C:HIS700 3.3 25.8 1.0
C29 C:7881 3.4 25.3 1.0
O C:HOH2005 3.4 28.1 1.0
CD2 C:HIS656 3.7 25.7 1.0
C27 C:7881 4.0 25.1 1.0
CD2 C:HIS700 4.0 25.9 1.0
CE1 C:HIS656 4.0 24.7 1.0
CG C:ASP697 4.1 22.3 1.0
OD2 C:ASP697 4.2 22.7 1.0
ZN C:ZN1001 4.3 26.2 1.0
CE1 C:HIS700 4.3 25.8 1.0
O C:HOH2008 4.3 13.6 1.0
C30 C:7881 4.3 25.8 1.0
OE2 C:GLU727 4.6 23.3 1.0
CG C:HIS656 4.7 25.3 1.0
ND1 C:HIS656 4.8 24.5 1.0
C26 C:7881 4.8 25.2 1.0
C25 C:7881 5.0 25.5 1.0

Magnesium binding site 4 out of 4 in 4d09

Go back to Magnesium Binding Sites List in 4d09
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:Mg1002

b:21.8
occ:1.00
 O D:HOH2032 2.2 11.6 1.0
O D:HOH2023 2.4 21.7 1.0
OD1 D:ASP697 2.4 24.1 1.0
O D:HOH2024 2.4 10.1 1.0
O D:HOH2015 2.5 20.0 1.0
OE2 D:GLU727 3.1 24.5 1.0
NE2 D:HIS730 3.5 27.4 1.0
O D:HOH2025 3.6 12.7 1.0
CG D:ASP697 3.6 24.0 1.0
NE2 D:HIS700 3.7 27.0 1.0
CD2 D:HIS730 3.8 26.8 1.0
CD2 D:HIS700 3.9 27.6 1.0
CD D:GLU727 4.1 24.6 1.0
OD2 D:ASP697 4.2 23.3 1.0
O D:HIS696 4.3 23.9 1.0
OG1 D:THR768 4.4 22.3 1.0
CG D:GLU727 4.4 25.0 1.0
ZN D:ZN1001 4.7 28.0 1.0
C28 D:7881 4.7 25.8 1.0
CE1 D:HIS730 4.8 27.1 1.0
CB D:ASP697 4.8 24.3 1.0
CB D:THR768 4.8 23.6 1.0
CA D:ASP697 4.9 24.6 1.0
O D:HOH2016 5.0 21.9 1.0
O D:THR768 5.0 24.7 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 07:22:48 2025

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