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

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

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

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with [2- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethynyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol, PDB code: 5sff 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) 43.41 / 2.16
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 134.927, 134.927, 235.164, 90, 90, 120
R / Rfree (%) 17.3 / 22.7

Other elements in 5sff:

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

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- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethynyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol (pdb code 5sff). 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- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethynyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol, PDB code: 5sff:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sff

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Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with [2- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethynyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol


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- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethynyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg803

b:33.9
occ:1.00
 O A:HOH961 2.0 38.3 1.0
O A:HOH976 2.0 34.1 1.0
OD1 A:ASP564 2.0 31.3 1.0
O A:HOH909 2.0 30.3 1.0
O A:HOH921 2.1 31.9 1.0
O A:HOH913 2.2 31.5 1.0
CG A:ASP564 3.1 32.4 1.0
OD2 A:ASP564 3.5 35.9 1.0
ZN A:ZN802 3.8 41.0 1.0
O A:HOH963 3.9 38.8 1.0
OE2 A:GLU592 4.0 41.3 1.0
NE2 A:HIS595 4.0 32.2 1.0
O A:HOH972 4.3 43.6 1.0
OG1 A:THR633 4.3 43.7 1.0
CD2 A:HIS563 4.3 36.0 1.0
CD2 A:HIS567 4.3 36.1 1.0
O A:HIS563 4.3 37.3 1.0
CD2 A:HIS595 4.4 31.3 1.0
CB A:ASP564 4.4 33.1 1.0
O A:THR633 4.5 39.1 1.0
NE2 A:HIS567 4.5 35.1 1.0
CD2 A:HIS525 4.6 37.1 1.0
NE2 A:HIS525 4.6 42.6 1.0
OD2 A:ASP674 4.6 38.4 1.0
NE2 A:HIS563 4.7 35.0 1.0
CB A:THR633 4.7 39.8 1.0
CA A:ASP564 4.8 36.5 1.0
CG A:GLU592 4.8 38.2 1.0
CD A:GLU592 4.8 39.2 1.0

Magnesium binding site 2 out of 4 in 5sff

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


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- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethynyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg803

b:32.9
occ:1.00
 O B:HOH927 2.0 37.1 1.0
O B:HOH974 2.0 29.4 1.0
O B:HOH930 2.0 26.3 1.0
O B:HOH958 2.1 27.3 1.0
O B:HOH911 2.1 28.2 1.0
OD1 B:ASP564 2.1 33.3 1.0
CG B:ASP564 3.1 30.9 1.0
OD2 B:ASP564 3.4 35.8 1.0
ZN B:ZN802 3.7 38.9 1.0
O B:HOH948 4.0 40.4 1.0
OE2 B:GLU592 4.0 37.3 1.0
NE2 B:HIS595 4.0 34.5 1.0
OG1 B:THR633 4.1 33.9 1.0
CD2 B:HIS563 4.2 34.6 1.0
O B:HOH961 4.2 42.8 1.0
O B:HIS563 4.3 39.1 1.0
CD2 B:HIS595 4.3 37.4 1.0
CD2 B:HIS567 4.3 33.3 1.0
OD2 B:ASP674 4.4 34.3 1.0
CB B:ASP564 4.5 34.6 1.0
NE2 B:HIS563 4.5 36.0 1.0
O B:THR633 4.5 37.0 1.0
NE2 B:HIS567 4.5 32.8 1.0
CD2 B:HIS525 4.6 35.6 1.0
CB B:THR633 4.6 36.2 1.0
NE2 B:HIS525 4.7 37.1 1.0
CA B:ASP564 4.8 35.9 1.0
CG B:GLU592 4.8 32.4 1.0
CD B:GLU592 4.8 36.0 1.0

Magnesium binding site 3 out of 4 in 5sff

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


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- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethynyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg803

b:33.1
occ:1.00
 O C:HOH947 2.0 31.8 1.0
O C:HOH919 2.1 30.9 1.0
OD1 C:ASP564 2.1 34.2 1.0
O C:HOH929 2.1 33.6 1.0
O C:HOH935 2.1 33.8 1.0
O C:HOH970 2.2 32.7 1.0
CG C:ASP564 3.1 33.9 1.0
OD2 C:ASP564 3.5 35.9 1.0
ZN C:ZN802 3.7 38.7 1.0
O C:HOH990 3.9 51.9 1.0
O C:HOH950 3.9 44.0 1.0
OE2 C:GLU592 4.0 39.1 1.0
NE2 C:HIS595 4.1 37.1 1.0
OG1 C:THR633 4.1 36.5 1.0
CD2 C:HIS567 4.2 36.5 1.0
O C:HOH934 4.2 39.7 1.0
CD2 C:HIS563 4.3 28.3 1.0
O C:HIS563 4.3 32.0 1.0
OD2 C:ASP674 4.4 35.9 1.0
NE2 C:HIS567 4.4 35.5 1.0
CD2 C:HIS595 4.4 35.9 1.0
O C:THR633 4.4 37.9 1.0
CB C:ASP564 4.4 30.1 1.0
CB C:THR633 4.6 37.3 1.0
NE2 C:HIS563 4.7 31.9 1.0
CD2 C:HIS525 4.7 38.5 1.0
NE2 C:HIS525 4.7 38.9 1.0
CA C:ASP564 4.8 33.8 1.0
CG C:GLU592 4.8 35.4 1.0
CD C:GLU592 4.9 36.5 1.0

Magnesium binding site 4 out of 4 in 5sff

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


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- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethynyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg803

b:47.9
occ:1.00
 O D:HOH922 1.9 50.6 1.0
OD1 D:ASP564 2.0 50.6 1.0
O D:HOH914 2.1 41.7 1.0
O D:HOH907 2.1 49.5 1.0
O D:HOH918 2.1 38.6 1.0
O D:HOH901 2.1 45.0 1.0
CG D:ASP564 3.0 48.1 1.0
OD2 D:ASP564 3.4 58.6 1.0
ZN D:ZN802 3.8 54.3 1.0
O D:HOH915 3.8 49.2 1.0
NE2 D:HIS595 3.9 52.9 1.0
OE2 D:GLU592 4.0 55.0 1.0
O D:HOH925 4.1 56.1 1.0
CD2 D:HIS567 4.2 49.1 1.0
OG1 D:THR633 4.3 52.0 1.0
CD2 D:HIS595 4.3 56.2 1.0
CD2 D:HIS563 4.3 44.6 1.0
NE2 D:HIS567 4.4 55.9 1.0
CB D:ASP564 4.4 48.5 1.0
O D:HIS563 4.4 50.5 1.0
CD2 D:HIS525 4.5 55.2 1.0
O D:THR633 4.5 53.5 1.0
NE2 D:HIS525 4.5 61.7 1.0
OD2 D:ASP674 4.6 53.9 1.0
NE2 D:HIS563 4.7 46.0 1.0
CA D:ASP564 4.8 46.0 1.0
CB D:THR633 4.8 52.5 1.0
CD D:GLU592 4.9 58.9 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 03:33:29 2024

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