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Magnesium in PDB 5sf7: Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(2- Chlorophenyl)-8-Methoxy-3,4-Dimethylimidazo[1,5-A]Quinazolin-5-One

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(2- Chlorophenyl)-8-Methoxy-3,4-Dimethylimidazo[1,5-A]Quinazolin-5-One

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(2- Chlorophenyl)-8-Methoxy-3,4-Dimethylimidazo[1,5-A]Quinazolin-5-One:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(2- Chlorophenyl)-8-Methoxy-3,4-Dimethylimidazo[1,5-A]Quinazolin-5-One, PDB code: 5sf7 was solved by C.Joseph, A.Flohr, J.Benz, D.Schlatter, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.52 / 2.08
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.284, 135.284, 235.352, 90, 90, 120
R / Rfree (%) 18.2 / 22.9

Other elements in 5sf7:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(2- Chlorophenyl)-8-Methoxy-3,4-Dimethylimidazo[1,5-A]Quinazolin-5-One also contains other interesting chemical elements:

Zinc (Zn) 4 atoms
Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(2- Chlorophenyl)-8-Methoxy-3,4-Dimethylimidazo[1,5-A]Quinazolin-5-One (pdb code 5sf7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(2- Chlorophenyl)-8-Methoxy-3,4-Dimethylimidazo[1,5-A]Quinazolin-5-One, PDB code: 5sf7:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sf7

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Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(2- Chlorophenyl)-8-Methoxy-3,4-Dimethylimidazo[1,5-A]Quinazolin-5-One


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(2- Chlorophenyl)-8-Methoxy-3,4-Dimethylimidazo[1,5-A]Quinazolin-5-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:23.8
occ:1.00
 OD1 A:ASP564 2.0 23.1 1.0
O A:HOH939 2.0 29.4 1.0
O A:HOH999 2.0 22.3 1.0
O A:HOH928 2.0 21.2 1.0
O A:HOH951 2.2 24.0 1.0
O A:HOH944 2.2 21.1 1.0
CG A:ASP564 3.0 23.6 1.0
OD2 A:ASP564 3.4 23.3 1.0
ZN A:ZN801 3.9 28.6 1.0
NE2 A:HIS595 4.0 28.0 1.0
OE2 A:GLU592 4.1 27.6 1.0
O A:HOH1001 4.1 22.8 1.0
O A:HOH987 4.2 26.4 1.0
CD2 A:HIS563 4.3 24.1 1.0
OG1 A:THR633 4.3 29.4 1.0
CD2 A:HIS567 4.3 25.6 1.0
CD2 A:HIS595 4.3 23.9 1.0
CB A:ASP564 4.3 22.1 1.0
OD2 A:ASP674 4.4 31.4 1.0
O A:HIS563 4.4 23.3 1.0
NE2 A:HIS567 4.4 27.5 1.0
O A:THR633 4.4 24.8 1.0
C22 A:IJN803 4.6 31.3 1.0
NE2 A:HIS563 4.6 25.8 1.0
CG A:GLU592 4.7 25.8 1.0
CB A:THR633 4.7 27.4 1.0
CA A:ASP564 4.8 22.6 1.0
NE2 A:HIS525 4.8 24.6 1.0
CD A:GLU592 4.8 27.9 1.0
CD2 A:HIS525 4.8 25.0 1.0

Magnesium binding site 2 out of 4 in 5sf7

Go back to Magnesium Binding Sites List in 5sf7
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(2- Chlorophenyl)-8-Methoxy-3,4-Dimethylimidazo[1,5-A]Quinazolin-5-One


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(2- Chlorophenyl)-8-Methoxy-3,4-Dimethylimidazo[1,5-A]Quinazolin-5-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:25.2
occ:1.00
 O B:HOH941 1.9 19.5 1.0
OD1 B:ASP564 2.0 23.9 1.0
O B:HOH942 2.0 21.6 1.0
O B:HOH963 2.1 19.8 1.0
O B:HOH980 2.1 19.5 1.0
O B:HOH975 2.1 20.1 1.0
CG B:ASP564 3.0 25.4 1.0
OD2 B:ASP564 3.5 24.0 1.0
ZN B:ZN801 3.8 27.6 1.0
NE2 B:HIS595 4.1 25.7 1.0
OE2 B:GLU592 4.1 28.5 1.0
O B:HOH966 4.1 22.6 1.0
CD2 B:HIS563 4.2 25.4 1.0
CD2 B:HIS567 4.2 23.0 1.0
OG1 B:THR633 4.2 26.3 1.0
CD2 B:HIS595 4.3 28.1 1.0
NE2 B:HIS567 4.3 23.9 1.0
O B:HOH1003 4.3 24.6 1.0
O B:HIS563 4.3 25.3 1.0
CB B:ASP564 4.4 24.9 1.0
OD2 B:ASP674 4.4 26.2 1.0
O B:THR633 4.5 23.5 1.0
C22 B:IJN803 4.5 29.9 1.0
NE2 B:HIS563 4.6 23.9 1.0
NE2 B:HIS525 4.6 25.1 1.0
CD2 B:HIS525 4.7 25.1 1.0
CB B:THR633 4.7 26.3 1.0
CA B:ASP564 4.7 24.7 1.0
CG B:GLU592 4.8 26.5 1.0
CD B:GLU592 4.9 27.5 1.0
C23 B:IJN803 5.0 31.5 1.0

Magnesium binding site 3 out of 4 in 5sf7

Go back to Magnesium Binding Sites List in 5sf7
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(2- Chlorophenyl)-8-Methoxy-3,4-Dimethylimidazo[1,5-A]Quinazolin-5-One


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(2- Chlorophenyl)-8-Methoxy-3,4-Dimethylimidazo[1,5-A]Quinazolin-5-One within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:26.2
occ:1.00
 O C:HOH1001 2.0 23.6 1.0
O C:HOH944 2.1 29.1 1.0
OD1 C:ASP564 2.1 27.2 1.0
O C:HOH1024 2.1 23.8 1.0
O C:HOH931 2.1 23.6 1.0
O C:HOH950 2.2 22.4 1.0
CG C:ASP564 3.1 27.4 1.0
OD2 C:ASP564 3.5 27.2 1.0
ZN C:ZN801 3.9 31.8 1.0
OE2 C:GLU592 3.9 32.5 1.0
NE2 C:HIS595 4.0 26.8 1.0
O C:HOH1010 4.0 27.3 1.0
O C:HOH1019 4.2 25.3 1.0
CD2 C:HIS567 4.2 25.7 1.0
CD2 C:HIS563 4.3 25.5 1.0
O C:HIS563 4.3 25.2 1.0
CD2 C:HIS595 4.3 26.9 1.0
NE2 C:HIS567 4.4 28.1 1.0
OG1 C:THR633 4.4 28.6 1.0
CB C:ASP564 4.4 24.2 1.0
OD2 C:ASP674 4.5 31.5 1.0
C22 C:IJN803 4.5 36.4 1.0
O C:THR633 4.5 26.7 1.0
NE2 C:HIS563 4.6 27.5 1.0
CB C:THR633 4.7 28.3 1.0
NE2 C:HIS525 4.7 32.7 1.0
CA C:ASP564 4.7 24.8 1.0
CD2 C:HIS525 4.8 32.6 1.0
CG C:GLU592 4.8 29.6 1.0
CD C:GLU592 4.8 32.9 1.0
C23 C:IJN803 5.0 32.6 1.0

Magnesium binding site 4 out of 4 in 5sf7

Go back to Magnesium Binding Sites List in 5sf7
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(2- Chlorophenyl)-8-Methoxy-3,4-Dimethylimidazo[1,5-A]Quinazolin-5-One


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(2- Chlorophenyl)-8-Methoxy-3,4-Dimethylimidazo[1,5-A]Quinazolin-5-One within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:31.5
occ:1.00
 O D:HOH964 2.0 25.3 1.0
OD1 D:ASP564 2.1 29.8 1.0
O D:HOH986 2.1 31.6 1.0
O D:HOH926 2.1 29.7 1.0
O D:HOH930 2.1 26.9 1.0
O D:HOH933 2.2 27.5 1.0
CG D:ASP564 3.1 29.7 1.0
OD2 D:ASP564 3.4 33.4 1.0
O D:HOH981 3.9 29.7 1.0
ZN D:ZN801 3.9 35.7 1.0
OE2 D:GLU592 4.0 33.1 1.0
NE2 D:HIS595 4.0 35.8 1.0
O D:HOH958 4.1 28.5 1.0
CD2 D:HIS567 4.2 38.3 1.0
CD2 D:HIS595 4.3 37.4 1.0
OG1 D:THR633 4.3 32.0 1.0
O D:HIS563 4.3 29.3 1.0
CD2 D:HIS563 4.4 27.5 1.0
CB D:ASP564 4.4 29.7 1.0
NE2 D:HIS567 4.4 33.1 1.0
C22 D:IJN803 4.5 41.6 1.0
O D:THR633 4.5 39.3 1.0
OD2 D:ASP674 4.6 38.3 1.0
CG D:GLU592 4.7 34.2 1.0
CA D:ASP564 4.7 27.8 1.0
CD D:GLU592 4.8 36.6 1.0
CD2 D:HIS525 4.8 34.7 1.0
NE2 D:HIS525 4.8 40.0 1.0
NE2 D:HIS563 4.8 25.4 1.0
CB D:THR633 4.8 31.9 1.0

Reference:

A.Tosstorff, M.G.Rudolph, J.C.Cole, M.Reutlinger, C.Kramer, H.Schaffhauser, A.Nilly, A.Flohr, B.Kuhn. A High Quality, Industrial Data Set For Binding Affinity Prediction: Performance Comparison in Different Early Drug Discovery Scenarios. J.Comput.Aided Mol.Des. V. 36 753 2022.
ISSN: ESSN 1573-4951
PubMed: 36153472
DOI: 10.1007/S10822-022-00478-X
Page generated: Mon Sep 30 03:30:43 2024

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