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Magnesium in PDB 5sed: Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[6- Chloro-2-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Quinazolin-4- Yl]Morpholine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[6- Chloro-2-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Quinazolin-4- Yl]Morpholine

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[6- Chloro-2-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Quinazolin-4- Yl]Morpholine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[6- Chloro-2-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Quinazolin-4- Yl]Morpholine, PDB code: 5sed was solved by C.Joseph, K.Groebke-Zbinden, 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) 43.49 / 2.32
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.193, 135.193, 235.868, 90, 90, 120
R / Rfree (%) 19.2 / 24.2

Other elements in 5sed:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[6- Chloro-2-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Quinazolin-4- Yl]Morpholine also contains other interesting chemical elements:

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

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[6- Chloro-2-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Quinazolin-4- Yl]Morpholine (pdb code 5sed). 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 4-[6- Chloro-2-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Quinazolin-4- Yl]Morpholine, PDB code: 5sed:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sed

Go back to Magnesium Binding Sites List in 5sed
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[6- Chloro-2-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Quinazolin-4- Yl]Morpholine


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 4-[6- Chloro-2-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Quinazolin-4- Yl]Morpholine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:24.6
occ:1.00
 O A:HOH965 1.8 20.6 1.0
OD1 A:ASP564 1.9 23.4 1.0
O A:HOH934 2.0 20.7 1.0
O A:HOH938 2.1 25.0 1.0
O A:HOH929 2.1 20.4 1.0
O A:HOH907 2.1 35.1 1.0
CG A:ASP564 2.9 25.4 1.0
OD2 A:ASP564 3.3 25.3 1.0
ZN A:ZN801 3.8 31.2 1.0
OE2 A:GLU592 3.9 29.4 1.0
O A:HOH991 4.0 45.1 1.0
O A:HOH946 4.0 36.3 1.0
NE2 A:HIS595 4.1 27.6 1.0
CD2 A:HIS567 4.2 30.7 1.0
CB A:ASP564 4.3 25.9 1.0
CD2 A:HIS563 4.3 25.8 1.0
O A:HOH981 4.4 34.2 1.0
CD2 A:HIS595 4.4 27.7 1.0
NE2 A:HIS567 4.4 30.6 1.0
O A:HIS563 4.4 29.0 1.0
OG1 A:THR633 4.4 26.4 1.0
OD2 A:ASP674 4.5 40.9 1.0
CD2 A:HIS525 4.6 29.7 1.0
O A:THR633 4.6 27.1 1.0
NE2 A:HIS525 4.6 28.4 1.0
NE2 A:HIS563 4.7 25.0 1.0
CB A:THR633 4.7 24.7 1.0
CA A:ASP564 4.7 27.4 1.0
CD A:GLU592 4.8 29.6 1.0
CG A:GLU592 4.8 28.3 1.0

Magnesium binding site 2 out of 4 in 5sed

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Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[6- Chloro-2-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Quinazolin-4- Yl]Morpholine


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 4-[6- Chloro-2-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Quinazolin-4- Yl]Morpholine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:21.4
occ:1.00
 O B:HOH914 1.9 22.2 1.0
O B:HOH982 1.9 18.9 1.0
O B:HOH903 2.0 21.3 1.0
O B:HOH923 2.0 19.5 1.0
OD1 B:ASP564 2.1 22.1 1.0
O B:HOH929 2.1 16.2 1.0
CG B:ASP564 3.2 23.6 1.0
OD2 B:ASP564 3.6 23.9 1.0
OE2 B:GLU592 3.7 29.5 1.0
ZN B:ZN801 3.9 31.1 1.0
O B:HOH956 3.9 29.8 1.0
NE2 B:HIS595 4.1 27.6 1.0
OG1 B:THR633 4.2 26.2 1.0
O B:HOH954 4.2 31.5 1.0
CD2 B:HIS563 4.2 27.3 1.0
CD2 B:HIS567 4.3 24.4 1.0
NE2 B:HIS567 4.3 24.7 1.0
O B:THR633 4.3 27.1 1.0
OD2 B:ASP674 4.4 28.7 1.0
CD2 B:HIS595 4.4 27.6 1.0
CB B:ASP564 4.5 22.6 1.0
O B:HIS563 4.5 26.3 1.0
CG B:GLU592 4.5 30.8 1.0
CD B:GLU592 4.6 30.8 1.0
NE2 B:HIS563 4.6 25.9 1.0
CB B:THR633 4.6 24.2 1.0
NE2 B:HIS525 4.6 28.9 1.0
CD2 B:HIS525 4.6 27.2 1.0
CA B:ASP564 4.8 24.2 1.0
C B:THR633 5.0 23.7 1.0

Magnesium binding site 3 out of 4 in 5sed

Go back to Magnesium Binding Sites List in 5sed
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[6- Chloro-2-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Quinazolin-4- Yl]Morpholine


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 4-[6- Chloro-2-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Quinazolin-4- Yl]Morpholine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:23.4
occ:1.00
 OD1 C:ASP564 2.0 30.2 1.0
O C:HOH988 2.1 26.7 1.0
O C:HOH956 2.1 28.9 1.0
O C:HOH912 2.1 22.4 1.0
O C:HOH930 2.2 20.2 1.0
O C:HOH954 2.2 31.2 1.0
CG C:ASP564 3.0 27.0 1.0
OD2 C:ASP564 3.4 25.9 1.0
ZN C:ZN801 3.8 33.4 1.0
CD2 C:HIS567 3.9 24.1 1.0
O C:HOH975 4.0 31.5 1.0
NE2 C:HIS567 4.1 25.0 1.0
OE2 C:GLU592 4.1 27.0 1.0
NE2 C:HIS595 4.2 31.2 1.0
O C:HOH977 4.3 34.9 1.0
CD2 C:HIS563 4.3 29.0 1.0
CB C:ASP564 4.4 25.6 1.0
CD2 C:HIS525 4.4 34.1 1.0
NE2 C:HIS525 4.5 30.5 1.0
CD2 C:HIS595 4.5 32.8 1.0
OD2 C:ASP674 4.5 27.9 1.0
O C:HIS563 4.5 23.7 1.0
OG1 C:THR633 4.6 27.7 1.0
NE2 C:HIS563 4.7 31.1 1.0
O C:THR633 4.7 29.2 1.0
CA C:ASP564 4.8 26.6 1.0
CG C:GLU592 4.9 29.9 1.0
CB C:THR633 4.9 29.9 1.0
CD C:GLU592 4.9 30.4 1.0

Magnesium binding site 4 out of 4 in 5sed

Go back to Magnesium Binding Sites List in 5sed
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[6- Chloro-2-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Quinazolin-4- Yl]Morpholine


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 4-[6- Chloro-2-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Quinazolin-4- Yl]Morpholine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:38.8
occ:1.00
 OD1 D:ASP564 2.0 45.4 1.0
O D:HOH910 2.1 36.7 1.0
O D:HOH922 2.2 33.0 1.0
O D:HOH909 2.2 26.9 1.0
O D:HOH936 2.2 32.6 1.0
O D:HOH902 2.3 32.4 1.0
CG D:ASP564 3.0 46.1 1.0
OD2 D:ASP564 3.3 55.3 1.0
O D:HOH912 3.9 40.8 1.0
ZN D:ZN801 3.9 44.5 1.0
O D:HOH934 4.0 38.8 1.0
OE2 D:GLU592 4.0 39.4 1.0
NE2 D:HIS595 4.0 47.7 1.0
CD2 D:HIS567 4.0 42.6 1.0
NE2 D:HIS567 4.2 43.6 1.0
OG1 D:THR633 4.2 38.3 1.0
CD2 D:HIS595 4.3 49.5 1.0
CB D:ASP564 4.3 41.5 1.0
CD2 D:HIS563 4.4 34.4 1.0
O D:HIS563 4.4 36.2 1.0
CD2 D:HIS525 4.5 46.1 1.0
OD2 D:ASP674 4.5 40.5 1.0
NE2 D:HIS525 4.6 44.4 1.0
CA D:ASP564 4.7 41.8 1.0
O D:THR633 4.7 45.8 1.0
CD D:GLU592 4.8 45.4 1.0
NE2 D:HIS563 4.8 34.2 1.0
CG D:GLU592 4.8 46.4 1.0
CB D:THR633 4.8 40.8 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 03:20:53 2024

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