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Magnesium in PDB 5ser: Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- (2-Fluoroethyl)-4-N,2-Dimethyl-3-N-(2-Phenyl-[1,2,4]Triazolo[1,5- A]Pyridin-7-Yl)Pyrazole-3,4-Dicarboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- (2-Fluoroethyl)-4-N,2-Dimethyl-3-N-(2-Phenyl-[1,2,4]Triazolo[1,5- A]Pyridin-7-Yl)Pyrazole-3,4-Dicarboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- (2-Fluoroethyl)-4-N,2-Dimethyl-3-N-(2-Phenyl-[1,2,4]Triazolo[1,5- A]Pyridin-7-Yl)Pyrazole-3,4-Dicarboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- (2-Fluoroethyl)-4-N,2-Dimethyl-3-N-(2-Phenyl-[1,2,4]Triazolo[1,5- A]Pyridin-7-Yl)Pyrazole-3,4-Dicarboxamide, PDB code: 5ser was solved by C.Joseph, A.Flohr, 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) 43.50 / 2.25
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.109, 135.109, 234.956, 90, 90, 120
R / Rfree (%) 17.2 / 23.3

Other elements in 5ser:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- (2-Fluoroethyl)-4-N,2-Dimethyl-3-N-(2-Phenyl-[1,2,4]Triazolo[1,5- A]Pyridin-7-Yl)Pyrazole-3,4-Dicarboxamide also contains other interesting chemical elements:

Zinc (Zn) 4 atoms
Fluorine (F) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- (2-Fluoroethyl)-4-N,2-Dimethyl-3-N-(2-Phenyl-[1,2,4]Triazolo[1,5- A]Pyridin-7-Yl)Pyrazole-3,4-Dicarboxamide (pdb code 5ser). 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-N- (2-Fluoroethyl)-4-N,2-Dimethyl-3-N-(2-Phenyl-[1,2,4]Triazolo[1,5- A]Pyridin-7-Yl)Pyrazole-3,4-Dicarboxamide, PDB code: 5ser:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5ser

Go back to Magnesium Binding Sites List in 5ser
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- (2-Fluoroethyl)-4-N,2-Dimethyl-3-N-(2-Phenyl-[1,2,4]Triazolo[1,5- A]Pyridin-7-Yl)Pyrazole-3,4-Dicarboxamide


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-N- (2-Fluoroethyl)-4-N,2-Dimethyl-3-N-(2-Phenyl-[1,2,4]Triazolo[1,5- A]Pyridin-7-Yl)Pyrazole-3,4-Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:34.2
occ:1.00
 O A:HOH967 1.9 28.5 1.0
O A:HOH916 1.9 29.0 1.0
OD1 A:ASP564 2.0 35.0 1.0
O A:HOH937 2.0 32.6 1.0
O A:HOH941 2.0 30.9 1.0
O A:HOH933 2.1 34.2 1.0
CG A:ASP564 3.0 33.8 1.0
OD2 A:ASP564 3.4 36.5 1.0
ZN A:ZN801 3.8 42.2 1.0
O A:HOH956 3.9 35.4 1.0
O A:HOH977 4.1 60.0 1.0
NE2 A:HIS595 4.1 36.7 1.0
OE2 A:GLU592 4.1 40.4 1.0
O A:HOH921 4.1 47.4 1.0
CD2 A:HIS567 4.2 35.2 1.0
O A:HIS563 4.2 38.8 1.0
NE2 A:HIS567 4.3 30.4 1.0
CD2 A:HIS595 4.4 35.2 1.0
CB A:ASP564 4.4 31.3 1.0
CD2 A:HIS563 4.4 32.0 1.0
OG1 A:THR633 4.4 39.4 1.0
O A:THR633 4.5 37.9 1.0
NE2 A:HIS525 4.5 41.0 1.0
CD2 A:HIS525 4.6 35.0 1.0
NE2 A:HIS563 4.7 34.9 1.0
OD2 A:ASP674 4.7 38.7 1.0
CB A:THR633 4.7 31.6 1.0
CA A:ASP564 4.7 33.8 1.0
CG A:GLU592 4.8 34.7 1.0
CD A:GLU592 4.9 39.7 1.0

Magnesium binding site 2 out of 4 in 5ser

Go back to Magnesium Binding Sites List in 5ser
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- (2-Fluoroethyl)-4-N,2-Dimethyl-3-N-(2-Phenyl-[1,2,4]Triazolo[1,5- A]Pyridin-7-Yl)Pyrazole-3,4-Dicarboxamide


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-N- (2-Fluoroethyl)-4-N,2-Dimethyl-3-N-(2-Phenyl-[1,2,4]Triazolo[1,5- A]Pyridin-7-Yl)Pyrazole-3,4-Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:32.0
occ:1.00
 OD1 B:ASP564 2.0 32.7 1.0
O B:HOH927 2.0 35.3 1.0
O B:HOH955 2.0 27.7 1.0
O B:HOH970 2.1 27.6 1.0
O B:HOH926 2.1 28.6 1.0
O B:HOH903 2.2 29.5 1.0
CG B:ASP564 3.0 33.4 1.0
OD2 B:ASP564 3.4 34.7 1.0
ZN B:ZN801 3.7 40.8 1.0
O B:HOH956 4.0 41.0 1.0
O B:HOH984 4.0 60.6 1.0
NE2 B:HIS595 4.0 34.6 1.0
OE2 B:GLU592 4.0 34.5 1.0
CD2 B:HIS563 4.1 38.5 1.0
OG1 B:THR633 4.2 36.1 1.0
O B:HOH948 4.2 44.6 1.0
O B:HIS563 4.3 39.0 1.0
CD2 B:HIS595 4.3 43.1 1.0
CD2 B:HIS567 4.3 36.0 1.0
CB B:ASP564 4.4 32.5 1.0
NE2 B:HIS563 4.4 33.2 1.0
NE2 B:HIS567 4.5 37.8 1.0
OD2 B:ASP674 4.5 34.5 1.0
O B:THR633 4.6 38.8 1.0
CB B:THR633 4.6 35.8 1.0
CD2 B:HIS525 4.6 37.9 1.0
CA B:ASP564 4.7 37.7 1.0
NE2 B:HIS525 4.7 36.7 1.0
CG B:GLU592 4.8 35.5 1.0
CD B:GLU592 4.8 34.6 1.0
C B:HIS563 5.0 35.1 1.0

Magnesium binding site 3 out of 4 in 5ser

Go back to Magnesium Binding Sites List in 5ser
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- (2-Fluoroethyl)-4-N,2-Dimethyl-3-N-(2-Phenyl-[1,2,4]Triazolo[1,5- A]Pyridin-7-Yl)Pyrazole-3,4-Dicarboxamide


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-N- (2-Fluoroethyl)-4-N,2-Dimethyl-3-N-(2-Phenyl-[1,2,4]Triazolo[1,5- A]Pyridin-7-Yl)Pyrazole-3,4-Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:33.6
occ:1.00
 O C:HOH928 2.0 35.3 1.0
OD1 C:ASP564 2.0 33.4 1.0
O C:HOH959 2.0 38.2 1.0
O C:HOH929 2.1 29.6 1.0
O C:HOH942 2.1 35.4 1.0
O C:HOH978 2.2 33.9 1.0
CG C:ASP564 3.0 32.4 1.0
OD2 C:ASP564 3.4 36.4 1.0
ZN C:ZN801 3.7 40.2 1.0
O C:HOH951 3.9 42.6 1.0
NE2 C:HIS595 4.1 36.3 1.0
O C:HOH981 4.1 49.7 1.0
CD2 C:HIS567 4.1 32.3 1.0
O C:HOH953 4.2 36.8 1.0
OE2 C:GLU592 4.2 38.0 1.0
O C:HIS563 4.3 31.9 1.0
CD2 C:HIS563 4.3 32.1 1.0
NE2 C:HIS567 4.3 34.4 1.0
OG1 C:THR633 4.3 34.6 1.0
CB C:ASP564 4.4 26.6 1.0
CD2 C:HIS595 4.4 39.1 1.0
OD2 C:ASP674 4.5 37.0 1.0
O C:THR633 4.6 37.1 1.0
NE2 C:HIS525 4.7 42.3 1.0
CD2 C:HIS525 4.7 40.4 1.0
NE2 C:HIS563 4.7 33.1 1.0
CB C:THR633 4.7 34.7 1.0
CA C:ASP564 4.7 32.9 1.0
CG C:GLU592 4.9 36.1 1.0
CD C:GLU592 5.0 38.1 1.0

Magnesium binding site 4 out of 4 in 5ser

Go back to Magnesium Binding Sites List in 5ser
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- (2-Fluoroethyl)-4-N,2-Dimethyl-3-N-(2-Phenyl-[1,2,4]Triazolo[1,5- A]Pyridin-7-Yl)Pyrazole-3,4-Dicarboxamide


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-N- (2-Fluoroethyl)-4-N,2-Dimethyl-3-N-(2-Phenyl-[1,2,4]Triazolo[1,5- A]Pyridin-7-Yl)Pyrazole-3,4-Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:48.7
occ:1.00
 OD1 D:ASP564 2.0 52.3 1.0
O D:HOH911 2.0 34.9 1.0
O D:HOH902 2.1 48.2 1.0
O D:HOH907 2.1 39.8 1.0
O D:HOH908 2.1 43.0 1.0
O D:HOH903 2.2 47.9 1.0
CG D:ASP564 3.1 50.8 1.0
OD2 D:ASP564 3.5 61.4 1.0
OE2 D:GLU592 3.8 55.1 1.0
NE2 D:HIS595 3.9 56.1 1.0
ZN D:ZN801 4.0 56.5 1.0
CD2 D:HIS567 4.0 47.9 1.0
O D:HOH924 4.1 45.6 1.0
CD2 D:HIS595 4.3 58.3 1.0
NE2 D:HIS567 4.3 58.5 1.0
OG1 D:THR633 4.3 49.5 1.0
CB D:ASP564 4.4 44.7 1.0
CD2 D:HIS563 4.5 53.5 1.0
O D:HIS563 4.5 47.5 1.0
NE2 D:HIS525 4.6 61.4 1.0
CD2 D:HIS525 4.6 68.7 1.0
O D:THR633 4.7 51.4 1.0
CA D:ASP564 4.7 49.1 1.0
CD D:GLU592 4.7 57.2 1.0
CB D:THR633 4.8 53.1 1.0
OD2 D:ASP674 4.8 55.2 1.0
NE2 D:HIS563 4.9 44.1 1.0
CE1 D:HIS595 5.0 58.7 1.0
CG D:GLU592 5.0 59.1 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 03:27:16 2024

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