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Magnesium in PDB 5sfb: Crystal Structure of Human Phosphodiesterase 10 in Complex with N,2,3- Trimethyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethyl]Imidazo[1,2-B]Pyridazine-8-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with N,2,3- Trimethyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethyl]Imidazo[1,2-B]Pyridazine-8-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with N,2,3- Trimethyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethyl]Imidazo[1,2-B]Pyridazine-8-Carboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N,2,3- Trimethyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethyl]Imidazo[1,2-B]Pyridazine-8-Carboxamide, PDB code: 5sfb 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) 43.75 / 1.98
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.915, 135.915, 235.641, 90, 90, 120
R / Rfree (%) 17.5 / 22.3

Other elements in 5sfb:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N,2,3- Trimethyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethyl]Imidazo[1,2-B]Pyridazine-8-Carboxamide 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 N,2,3- Trimethyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethyl]Imidazo[1,2-B]Pyridazine-8-Carboxamide (pdb code 5sfb). 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 N,2,3- Trimethyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethyl]Imidazo[1,2-B]Pyridazine-8-Carboxamide, PDB code: 5sfb:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sfb

Go back to Magnesium Binding Sites List in 5sfb
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N,2,3- Trimethyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethyl]Imidazo[1,2-B]Pyridazine-8-Carboxamide


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 N,2,3- Trimethyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethyl]Imidazo[1,2-B]Pyridazine-8-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:26.6
occ:1.00
 OD1 A:ASP564 2.0 23.2 1.0
O A:HOH1011 2.0 28.4 1.0
O A:HOH981 2.1 24.1 1.0
O A:HOH955 2.1 24.5 1.0
O A:HOH938 2.2 26.6 1.0
O A:HOH952 2.2 22.3 1.0
CG A:ASP564 3.0 26.7 1.0
OD2 A:ASP564 3.4 27.5 1.0
ZN A:ZN801 3.8 30.4 1.0
O A:HOH963 3.9 37.7 1.0
NE2 A:HIS595 4.0 26.4 1.0
OE2 A:GLU592 4.0 27.6 1.0
O A:HOH1039 4.1 47.1 1.0
CD2 A:HIS567 4.2 27.9 1.0
OG1 A:THR633 4.3 27.9 1.0
O A:HOH980 4.3 34.1 1.0
CD2 A:HIS563 4.3 26.8 1.0
CD2 A:HIS595 4.3 23.7 1.0
O A:HIS563 4.4 27.4 1.0
CB A:ASP564 4.4 26.8 1.0
NE2 A:HIS567 4.5 26.6 1.0
CD2 A:HIS525 4.5 29.0 1.0
NE2 A:HIS525 4.5 32.0 1.0
O A:THR633 4.6 25.8 1.0
OD2 A:ASP674 4.7 37.1 1.0
NE2 A:HIS563 4.7 25.6 1.0
CB A:THR633 4.7 30.2 1.0
CA A:ASP564 4.7 26.3 1.0
CD A:GLU592 4.9 28.8 1.0
CG A:GLU592 4.9 28.1 1.0
CE1 A:HIS595 5.0 24.6 1.0

Magnesium binding site 2 out of 4 in 5sfb

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Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N,2,3- Trimethyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethyl]Imidazo[1,2-B]Pyridazine-8-Carboxamide


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 N,2,3- Trimethyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethyl]Imidazo[1,2-B]Pyridazine-8-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:25.6
occ:1.00
 O B:HOH955 2.0 25.4 1.0
O B:HOH945 2.0 20.7 1.0
O B:HOH1026 2.1 23.5 1.0
OD1 B:ASP564 2.1 24.7 1.0
O B:HOH980 2.1 21.0 1.0
O B:HOH907 2.2 25.2 1.0
CG B:ASP564 3.1 25.5 1.0
OD2 B:ASP564 3.4 24.5 1.0
ZN B:ZN801 3.8 29.8 1.0
O B:HOH976 3.9 39.1 1.0
OE2 B:GLU592 4.0 28.5 1.0
O B:HOH1061 4.0 43.3 1.0
NE2 B:HIS595 4.0 25.9 1.0
OG1 B:THR633 4.2 25.6 1.0
O B:HIS563 4.3 25.8 1.0
CD2 B:HIS567 4.3 27.7 1.0
O B:HOH947 4.3 28.3 1.0
CD2 B:HIS595 4.3 26.9 1.0
CD2 B:HIS563 4.3 23.6 1.0
CB B:ASP564 4.4 22.5 1.0
NE2 B:HIS567 4.5 25.1 1.0
OD2 B:ASP674 4.5 33.4 1.0
O B:THR633 4.5 25.0 1.0
CD2 B:HIS525 4.6 26.2 1.0
NE2 B:HIS525 4.7 31.6 1.0
NE2 B:HIS563 4.7 23.9 1.0
CB B:THR633 4.7 25.4 1.0
CA B:ASP564 4.7 23.4 1.0
CG B:GLU592 4.8 24.8 1.0
CD B:GLU592 4.9 24.7 1.0

Magnesium binding site 3 out of 4 in 5sfb

Go back to Magnesium Binding Sites List in 5sfb
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N,2,3- Trimethyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethyl]Imidazo[1,2-B]Pyridazine-8-Carboxamide


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 N,2,3- Trimethyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethyl]Imidazo[1,2-B]Pyridazine-8-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:26.6
occ:1.00
 O C:HOH936 2.0 23.9 1.0
OD1 C:ASP564 2.0 25.9 1.0
O C:HOH928 2.1 25.3 1.0
O C:HOH1027 2.1 23.3 1.0
O C:HOH976 2.1 29.0 1.0
O C:HOH932 2.2 26.9 1.0
CG C:ASP564 3.1 27.8 1.0
OD2 C:ASP564 3.5 25.4 1.0
ZN C:ZN801 3.8 31.5 1.0
O C:HOH968 3.9 43.7 1.0
O C:HOH1038 4.0 45.5 1.0
OE2 C:GLU592 4.0 28.8 1.0
NE2 C:HIS595 4.1 27.6 1.0
OG1 C:THR633 4.1 27.8 1.0
CD2 C:HIS567 4.3 28.9 1.0
CD2 C:HIS563 4.3 22.8 1.0
O C:HOH986 4.3 32.8 1.0
O C:HIS563 4.3 26.2 1.0
OD2 C:ASP674 4.4 34.2 1.0
CD2 C:HIS595 4.4 28.8 1.0
O C:THR633 4.4 30.6 1.0
CB C:ASP564 4.4 24.2 1.0
NE2 C:HIS567 4.5 26.3 1.0
CD2 C:HIS525 4.6 27.9 1.0
CB C:THR633 4.7 27.5 1.0
NE2 C:HIS563 4.7 24.6 1.0
NE2 C:HIS525 4.7 30.5 1.0
CA C:ASP564 4.8 25.5 1.0
CG C:GLU592 4.9 25.9 1.0
CD C:GLU592 4.9 25.4 1.0

Magnesium binding site 4 out of 4 in 5sfb

Go back to Magnesium Binding Sites List in 5sfb
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N,2,3- Trimethyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethyl]Imidazo[1,2-B]Pyridazine-8-Carboxamide


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 N,2,3- Trimethyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethyl]Imidazo[1,2-B]Pyridazine-8-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:38.6
occ:1.00
 O D:HOH939 2.1 30.7 1.0
O D:HOH944 2.1 31.1 1.0
OD1 D:ASP564 2.1 34.2 1.0
O D:HOH949 2.1 32.8 1.0
O D:HOH920 2.2 32.1 1.0
O D:HOH922 2.2 33.9 1.0
CG D:ASP564 3.1 34.9 1.0
OD2 D:ASP564 3.4 34.6 1.0
O D:HOH942 3.6 43.9 1.0
ZN D:ZN801 3.8 39.0 1.0
OE2 D:GLU592 4.0 37.0 1.0
NE2 D:HIS595 4.0 38.2 1.0
O D:HOH968 4.2 40.7 1.0
OG1 D:THR633 4.3 36.9 1.0
CD2 D:HIS567 4.3 41.7 1.0
CD2 D:HIS595 4.4 35.1 1.0
CD2 D:HIS563 4.4 31.6 1.0
NE2 D:HIS525 4.4 47.1 1.0
O D:HIS563 4.5 33.7 1.0
OD2 D:ASP674 4.5 41.0 1.0
CD2 D:HIS525 4.5 42.1 1.0
CB D:ASP564 4.5 31.7 1.0
NE2 D:HIS567 4.5 37.0 1.0
O D:THR633 4.6 42.7 1.0
CB D:THR633 4.8 37.4 1.0
NE2 D:HIS563 4.9 30.5 1.0
CA D:ASP564 4.9 29.6 1.0
CD D:GLU592 4.9 39.4 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: Tue Aug 12 19:27:20 2025

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