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Magnesium in PDB 5sf1: Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- (Difluoromethyl)-3-Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl) Ethynyl]Imidazo[1,2-B]Pyridazine

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

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

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- (Difluoromethyl)-3-Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl) Ethynyl]Imidazo[1,2-B]Pyridazine, PDB code: 5sf1 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) 43.74 / 2.11
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.436, 135.436, 235.715, 90, 90, 120
R / Rfree (%) 18.4 / 23.1

Other elements in 5sf1:

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

Fluorine (F) 8 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 2- (Difluoromethyl)-3-Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl) Ethynyl]Imidazo[1,2-B]Pyridazine (pdb code 5sf1). 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 2- (Difluoromethyl)-3-Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl) Ethynyl]Imidazo[1,2-B]Pyridazine, PDB code: 5sf1:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sf1

Go back to Magnesium Binding Sites List in 5sf1
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- (Difluoromethyl)-3-Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl) Ethynyl]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 2- (Difluoromethyl)-3-Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl) Ethynyl]Imidazo[1,2-B]Pyridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg803

b:28.6
occ:1.00
 O A:HOH967 1.9 25.1 1.0
OD1 A:ASP564 2.0 28.5 1.0
O A:HOH958 2.0 28.9 1.0
O A:HOH910 2.0 26.6 1.0
O A:HOH929 2.1 28.2 1.0
O A:HOH908 2.2 27.8 1.0
CG A:ASP564 3.1 30.2 1.0
OD2 A:ASP564 3.5 31.4 1.0
OE2 A:GLU592 3.8 35.0 1.0
ZN A:ZN802 3.8 36.1 1.0
NE2 A:HIS595 3.9 29.7 1.0
O A:HOH961 4.1 31.3 1.0
OG1 A:THR633 4.2 32.4 1.0
CD2 A:HIS595 4.3 30.4 1.0
CD2 A:HIS563 4.3 32.3 1.0
O A:HIS563 4.3 30.2 1.0
CD2 A:HIS567 4.4 35.2 1.0
O A:HOH960 4.4 36.5 1.0
CB A:ASP564 4.4 29.3 1.0
O A:THR633 4.5 34.5 1.0
NE2 A:HIS567 4.6 31.3 1.0
OD2 A:ASP674 4.7 35.9 1.0
CB A:THR633 4.7 31.4 1.0
CD2 A:HIS525 4.7 31.6 1.0
NE2 A:HIS525 4.7 35.0 1.0
CD A:GLU592 4.7 33.8 1.0
CA A:ASP564 4.8 31.6 1.0
NE2 A:HIS563 4.8 30.3 1.0
CG A:GLU592 4.8 32.4 1.0

Magnesium binding site 2 out of 4 in 5sf1

Go back to Magnesium Binding Sites List in 5sf1
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- (Difluoromethyl)-3-Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl) Ethynyl]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 2- (Difluoromethyl)-3-Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl) Ethynyl]Imidazo[1,2-B]Pyridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg803

b:33.2
occ:1.00
 O B:HOH924 2.0 31.2 1.0
O B:HOH944 2.0 24.9 1.0
O B:HOH913 2.1 25.0 1.0
O B:HOH934 2.1 27.0 1.0
OD1 B:ASP564 2.1 29.6 1.0
O B:HOH951 2.1 26.6 1.0
CG B:ASP564 3.2 29.0 1.0
OD2 B:ASP564 3.6 29.3 1.0
O B:HOH986 3.7 48.9 1.0
ZN B:ZN802 3.9 34.5 1.0
OE2 B:GLU592 3.9 33.8 1.0
NE2 B:HIS595 4.0 32.1 1.0
O B:HOH950 4.0 37.7 1.0
OG1 B:THR633 4.1 30.5 1.0
O B:HOH936 4.2 39.2 1.0
CD2 B:HIS567 4.2 31.1 1.0
CD2 B:HIS595 4.3 33.9 1.0
NE2 B:HIS567 4.3 28.4 1.0
O B:HIS563 4.3 34.5 1.0
CD2 B:HIS563 4.4 27.4 1.0
OD2 B:ASP674 4.5 31.7 1.0
CB B:ASP564 4.5 27.8 1.0
O B:THR633 4.5 31.0 1.0
CD2 B:HIS525 4.6 27.9 1.0
NE2 B:HIS525 4.6 32.5 1.0
NE2 B:HIS563 4.7 29.0 1.0
CG B:GLU592 4.7 28.8 1.0
CD B:GLU592 4.7 28.9 1.0
CB B:THR633 4.7 31.8 1.0
CA B:ASP564 4.8 30.9 1.0

Magnesium binding site 3 out of 4 in 5sf1

Go back to Magnesium Binding Sites List in 5sf1
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- (Difluoromethyl)-3-Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl) Ethynyl]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 2- (Difluoromethyl)-3-Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl) Ethynyl]Imidazo[1,2-B]Pyridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg803

b:31.2
occ:1.00
 O C:HOH959 2.0 31.0 1.0
O C:HOH915 2.0 28.9 1.0
O C:HOH931 2.1 28.3 1.0
OD1 C:ASP564 2.1 32.2 1.0
O C:HOH971 2.2 28.0 1.0
O C:HOH920 2.2 32.3 1.0
CG C:ASP564 3.1 30.5 1.0
OD2 C:ASP564 3.4 29.8 1.0
ZN C:ZN802 3.7 35.6 1.0
O C:HOH983 3.9 46.9 1.0
O C:HOH962 4.0 36.5 1.0
OE2 C:GLU592 4.0 30.0 1.0
NE2 C:HIS595 4.1 34.2 1.0
CD2 C:HIS567 4.1 33.7 1.0
OG1 C:THR633 4.2 31.4 1.0
CD2 C:HIS563 4.3 27.1 1.0
NE2 C:HIS567 4.3 31.4 1.0
O C:HOH961 4.3 36.9 1.0
O C:HIS563 4.3 31.1 1.0
OD2 C:ASP674 4.3 35.1 1.0
CD2 C:HIS595 4.4 33.1 1.0
O C:THR633 4.4 33.3 1.0
CB C:ASP564 4.5 27.6 1.0
NE2 C:HIS525 4.6 35.1 1.0
CD2 C:HIS525 4.7 35.3 1.0
CB C:THR633 4.7 31.6 1.0
NE2 C:HIS563 4.8 29.8 1.0
CG C:GLU592 4.8 32.2 1.0
CA C:ASP564 4.8 30.9 1.0
CD C:GLU592 4.9 31.1 1.0

Magnesium binding site 4 out of 4 in 5sf1

Go back to Magnesium Binding Sites List in 5sf1
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- (Difluoromethyl)-3-Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl) Ethynyl]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 2- (Difluoromethyl)-3-Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl) Ethynyl]Imidazo[1,2-B]Pyridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg803

b:48.4
occ:1.00
 O D:HOH932 2.0 37.9 1.0
O D:HOH920 2.1 41.3 1.0
O D:HOH933 2.1 45.1 1.0
OD1 D:ASP564 2.1 42.4 1.0
O D:HOH901 2.2 47.5 1.0
O D:HOH913 2.3 41.6 1.0
CG D:ASP564 3.1 40.8 1.0
OD2 D:ASP564 3.4 52.9 1.0
ZN D:ZN802 3.8 48.4 1.0
O D:HOH930 3.8 43.4 1.0
OE2 D:GLU592 4.0 49.0 1.0
O D:HOH936 4.0 44.1 1.0
NE2 D:HIS595 4.1 47.0 1.0
CD2 D:HIS567 4.3 47.9 1.0
OG1 D:THR633 4.3 41.2 1.0
CD2 D:HIS563 4.4 39.6 1.0
O D:HIS563 4.4 41.0 1.0
CD2 D:HIS595 4.5 48.1 1.0
CB D:ASP564 4.5 40.3 1.0
NE2 D:HIS567 4.5 42.8 1.0
OD2 D:ASP674 4.5 49.1 1.0
NE2 D:HIS525 4.6 55.8 1.0
CD2 D:HIS525 4.6 45.5 1.0
O D:THR633 4.7 46.2 1.0
CB D:THR633 4.7 45.9 1.0
NE2 D:HIS563 4.8 38.1 1.0
CD D:GLU592 4.8 46.8 1.0
CA D:ASP564 4.8 37.2 1.0
CG D:GLU592 4.9 50.0 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 03:30:09 2024

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