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Magnesium in PDB 5sem: Crystal Structure of Human Phosphodiesterase 10 in Complex with 3- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine, PDB code: 5sem 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) 43.57 / 2.10
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.449, 135.449, 235.505, 90, 90, 120
R / Rfree (%) 17.8 / 22.8

Other elements in 5sem:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine also contains other interesting chemical elements:

Fluorine (F) 12 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 3- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine (pdb code 5sem). 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 3- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine, PDB code: 5sem:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sem

Go back to Magnesium Binding Sites List in 5sem
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine


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 3- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:32.3
occ:1.00
 O A:HOH999 1.9 27.8 1.0
O A:HOH917 2.0 27.4 1.0
OD1 A:ASP564 2.0 29.7 1.0
O A:HOH984 2.1 29.4 1.0
O A:HOH954 2.2 29.6 1.0
O A:HOH928 2.2 30.9 1.0
CG A:ASP564 3.1 32.4 1.0
OD2 A:ASP564 3.5 37.8 1.0
ZN A:ZN801 3.8 38.2 1.0
O A:HOH982 3.9 35.2 1.0
OE2 A:GLU592 4.0 34.5 1.0
NE2 A:HIS595 4.0 29.5 1.0
O A:HOH1011 4.1 48.6 1.0
O A:HOH979 4.1 35.3 1.0
OG1 A:THR633 4.2 31.8 1.0
O A:HIS563 4.3 32.2 1.0
CD2 A:HIS567 4.3 35.0 1.0
CD2 A:HIS595 4.3 31.0 1.0
CD2 A:HIS563 4.4 32.9 1.0
CB A:ASP564 4.4 30.2 1.0
NE2 A:HIS567 4.5 31.6 1.0
O A:THR633 4.5 33.2 1.0
NE2 A:HIS525 4.7 37.8 1.0
CD2 A:HIS525 4.7 38.2 1.0
CB A:THR633 4.7 31.6 1.0
OD2 A:ASP674 4.7 38.6 1.0
CA A:ASP564 4.8 32.0 1.0
NE2 A:HIS563 4.8 34.5 1.0
CG A:GLU592 4.8 33.3 1.0
CD A:GLU592 4.8 34.7 1.0

Magnesium binding site 2 out of 4 in 5sem

Go back to Magnesium Binding Sites List in 5sem
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine


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 3- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:28.7
occ:1.00
 O B:HOH979 1.9 25.1 1.0
O B:HOH910 2.0 24.4 1.0
O B:HOH945 2.0 30.1 1.0
O B:HOH971 2.1 25.1 1.0
O B:HOH999 2.1 25.3 1.0
OD1 B:ASP564 2.2 29.6 1.0
CG B:ASP564 3.1 27.2 1.0
OD2 B:ASP564 3.5 29.1 1.0
O B:HOH1022 3.7 45.2 1.0
ZN B:ZN801 3.8 35.5 1.0
OE2 B:GLU592 3.9 31.2 1.0
O B:HOH952 3.9 34.1 1.0
NE2 B:HIS595 4.1 31.1 1.0
OG1 B:THR633 4.1 29.1 1.0
CD2 B:HIS563 4.2 28.5 1.0
O B:HIS563 4.2 34.6 1.0
CD2 B:HIS567 4.3 34.8 1.0
O B:HOH958 4.3 29.6 1.0
CD2 B:HIS595 4.3 31.4 1.0
NE2 B:HIS567 4.4 32.1 1.0
OD2 B:ASP674 4.4 30.9 1.0
O B:THR633 4.5 32.2 1.0
CB B:ASP564 4.5 26.5 1.0
NE2 B:HIS563 4.5 26.9 1.0
CB B:THR633 4.6 32.0 1.0
CD2 B:HIS525 4.6 29.6 1.0
NE2 B:HIS525 4.7 33.0 1.0
CD B:GLU592 4.8 32.1 1.0
CG B:GLU592 4.8 29.5 1.0
CA B:ASP564 4.8 30.1 1.0

Magnesium binding site 3 out of 4 in 5sem

Go back to Magnesium Binding Sites List in 5sem
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine


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 3- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:32.2
occ:1.00
 OD1 C:ASP564 2.0 29.6 1.0
O C:HOH933 2.0 34.3 1.0
O C:HOH971 2.1 29.1 1.0
O C:HOH982 2.1 27.6 1.0
O C:HOH917 2.1 27.6 1.0
O C:HOH1009 2.1 30.0 1.0
CG C:ASP564 3.1 30.6 1.0
OD2 C:ASP564 3.5 30.1 1.0
OE2 C:GLU592 3.8 32.4 1.0
ZN C:ZN801 3.8 37.1 1.0
O C:HOH1016 4.0 44.8 1.0
NE2 C:HIS595 4.0 34.4 1.0
O C:HOH964 4.1 35.1 1.0
OG1 C:THR633 4.2 30.9 1.0
CD2 C:HIS567 4.2 30.6 1.0
CD2 C:HIS563 4.2 28.8 1.0
O C:HIS563 4.3 29.4 1.0
CD2 C:HIS595 4.3 31.7 1.0
O C:HOH987 4.4 32.8 1.0
CB C:ASP564 4.4 29.0 1.0
NE2 C:HIS567 4.4 29.3 1.0
O C:THR633 4.5 34.2 1.0
OD2 C:ASP674 4.5 36.4 1.0
CB C:THR633 4.6 34.8 1.0
NE2 C:HIS563 4.7 32.1 1.0
CD C:GLU592 4.7 37.4 1.0
CG C:GLU592 4.7 34.9 1.0
NE2 C:HIS525 4.7 34.9 1.0
CD2 C:HIS525 4.7 36.4 1.0
CA C:ASP564 4.8 31.7 1.0

Magnesium binding site 4 out of 4 in 5sem

Go back to Magnesium Binding Sites List in 5sem
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine


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 3- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:43.4
occ:1.00
 O D:HOH940 2.0 33.7 1.0
O D:HOH950 2.0 40.3 1.0
O D:HOH938 2.0 36.5 1.0
OD1 D:ASP564 2.1 40.8 1.0
O D:HOH907 2.1 36.2 1.0
O D:HOH908 2.2 36.9 1.0
CG D:ASP564 3.1 39.4 1.0
OD2 D:ASP564 3.4 49.7 1.0
ZN D:ZN801 3.7 46.1 1.0
O D:HOH923 3.8 42.4 1.0
OE2 D:GLU592 3.9 41.5 1.0
O D:HOH946 3.9 47.7 1.0
NE2 D:HIS595 4.0 51.2 1.0
OG1 D:THR633 4.1 38.1 1.0
CD2 D:HIS567 4.2 41.5 1.0
CD2 D:HIS595 4.4 45.9 1.0
CD2 D:HIS563 4.4 35.2 1.0
O D:THR633 4.4 46.6 1.0
O D:HIS563 4.4 39.0 1.0
CD2 D:HIS525 4.5 45.2 1.0
NE2 D:HIS525 4.5 49.6 1.0
CB D:ASP564 4.5 41.4 1.0
NE2 D:HIS567 4.5 40.7 1.0
OD2 D:ASP674 4.5 46.1 1.0
CB D:THR633 4.7 44.0 1.0
CD D:GLU592 4.8 46.6 1.0
NE2 D:HIS563 4.8 32.0 1.0
CA D:ASP564 4.9 40.5 1.0
CG D:GLU592 4.9 47.1 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 03:23:47 2024

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