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Magnesium in PDB 5se3: Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Chloro-N-(2-Phenyl-[1,2,4]Triazolo[1,5-A]Pyridin-7-Yl)Pyridine-4- Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Chloro-N-(2-Phenyl-[1,2,4]Triazolo[1,5-A]Pyridin-7-Yl)Pyridine-4- Carboxamide

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

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Chloro-N-(2-Phenyl-[1,2,4]Triazolo[1,5-A]Pyridin-7-Yl)Pyridine-4- Carboxamide, PDB code: 5se3 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) 43.54 / 2.14
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.37, 135.37, 235.253, 90, 90, 120
R / Rfree (%) 18 / 22.6

Other elements in 5se3:

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

Chlorine (Cl) 4 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- Chloro-N-(2-Phenyl-[1,2,4]Triazolo[1,5-A]Pyridin-7-Yl)Pyridine-4- Carboxamide (pdb code 5se3). 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- Chloro-N-(2-Phenyl-[1,2,4]Triazolo[1,5-A]Pyridin-7-Yl)Pyridine-4- Carboxamide, PDB code: 5se3:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5se3

Go back to Magnesium Binding Sites List in 5se3
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Chloro-N-(2-Phenyl-[1,2,4]Triazolo[1,5-A]Pyridin-7-Yl)Pyridine-4- 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 2- Chloro-N-(2-Phenyl-[1,2,4]Triazolo[1,5-A]Pyridin-7-Yl)Pyridine-4- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:26.9
occ:1.00
 OD1 A:ASP564 2.0 25.3 1.0
O A:HOH1006 2.0 23.8 1.0
O A:HOH950 2.1 24.4 1.0
O A:HOH937 2.1 26.9 1.0
O A:HOH958 2.1 22.8 1.0
O A:HOH935 2.1 24.7 1.0
CG A:ASP564 2.9 23.9 1.0
OD2 A:ASP564 3.3 25.7 1.0
O A:HOH1017 3.7 48.6 1.0
ZN A:ZN801 3.8 31.6 1.0
OE2 A:GLU592 4.0 32.8 1.0
NE2 A:HIS595 4.0 31.3 1.0
O A:HOH964 4.0 37.0 1.0
CD2 A:HIS567 4.2 34.9 1.0
OG1 A:THR633 4.3 28.0 1.0
CD2 A:HIS563 4.3 25.3 1.0
CB A:ASP564 4.3 23.5 1.0
CD2 A:HIS595 4.3 30.4 1.0
O A:HIS563 4.4 28.7 1.0
O A:THR633 4.4 31.5 1.0
NE2 A:HIS567 4.4 27.1 1.0
O A:HOH963 4.4 34.3 1.0
OD2 A:ASP674 4.5 36.1 1.0
CD2 A:HIS525 4.6 28.5 1.0
NE2 A:HIS563 4.7 28.9 1.0
NE2 A:HIS525 4.7 29.0 1.0
CB A:THR633 4.7 27.1 1.0
CA A:ASP564 4.7 27.4 1.0
CD A:GLU592 4.8 32.0 1.0
CG A:GLU592 4.9 28.4 1.0

Magnesium binding site 2 out of 4 in 5se3

Go back to Magnesium Binding Sites List in 5se3
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Chloro-N-(2-Phenyl-[1,2,4]Triazolo[1,5-A]Pyridin-7-Yl)Pyridine-4- 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 2- Chloro-N-(2-Phenyl-[1,2,4]Triazolo[1,5-A]Pyridin-7-Yl)Pyridine-4- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:24.9
occ:1.00
 O B:HOH947 1.9 24.0 1.0
O B:HOH922 2.0 22.5 1.0
O B:HOH964 2.0 18.9 1.0
O B:HOH1012 2.0 22.1 1.0
OD1 B:ASP564 2.0 24.9 1.0
O B:HOH938 2.1 19.5 1.0
CG B:ASP564 3.1 24.7 1.0
OD2 B:ASP564 3.4 24.6 1.0
ZN B:ZN801 3.8 30.7 1.0
OE2 B:GLU592 3.9 29.6 1.0
O B:HOH982 4.0 31.6 1.0
NE2 B:HIS595 4.0 27.0 1.0
CD2 B:HIS563 4.2 24.5 1.0
OG1 B:THR633 4.2 25.4 1.0
CD2 B:HIS595 4.2 27.9 1.0
CD2 B:HIS567 4.3 26.3 1.0
O B:HOH1000 4.3 29.3 1.0
O B:HIS563 4.3 31.7 1.0
OD2 B:ASP674 4.4 27.2 1.0
CB B:ASP564 4.4 23.4 1.0
NE2 B:HIS567 4.4 26.8 1.0
NE2 B:HIS563 4.5 22.7 1.0
O B:THR633 4.6 28.7 1.0
CD2 B:HIS525 4.6 27.9 1.0
NE2 B:HIS525 4.6 26.9 1.0
CB B:THR633 4.7 26.8 1.0
CG B:GLU592 4.7 28.7 1.0
CA B:ASP564 4.8 24.7 1.0
CD B:GLU592 4.8 29.6 1.0

Magnesium binding site 3 out of 4 in 5se3

Go back to Magnesium Binding Sites List in 5se3
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Chloro-N-(2-Phenyl-[1,2,4]Triazolo[1,5-A]Pyridin-7-Yl)Pyridine-4- 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 2- Chloro-N-(2-Phenyl-[1,2,4]Triazolo[1,5-A]Pyridin-7-Yl)Pyridine-4- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:27.6
occ:1.00
 O C:HOH953 2.0 30.1 1.0
O C:HOH973 2.0 28.1 1.0
O C:HOH983 2.0 23.3 1.0
O C:HOH1019 2.1 23.9 1.0
OD1 C:ASP564 2.1 26.8 1.0
O C:HOH938 2.1 22.0 1.0
CG C:ASP564 3.1 28.1 1.0
OD2 C:ASP564 3.5 29.1 1.0
ZN C:ZN801 3.9 32.6 1.0
OE2 C:GLU592 3.9 30.8 1.0
O C:HOH1008 3.9 31.8 1.0
NE2 C:HIS595 4.0 27.6 1.0
O C:HOH994 4.2 31.6 1.0
CD2 C:HIS567 4.2 24.0 1.0
CD2 C:HIS595 4.3 26.6 1.0
CD2 C:HIS563 4.3 24.9 1.0
NE2 C:HIS567 4.4 24.6 1.0
OG1 C:THR633 4.4 28.6 1.0
O C:HIS563 4.4 25.6 1.0
CB C:ASP564 4.5 24.8 1.0
OD2 C:ASP674 4.5 32.6 1.0
O C:THR633 4.6 30.1 1.0
CD2 C:HIS525 4.7 33.8 1.0
NE2 C:HIS525 4.7 35.4 1.0
CG C:GLU592 4.7 28.9 1.0
CB C:THR633 4.8 26.5 1.0
CD C:GLU592 4.8 33.5 1.0
NE2 C:HIS563 4.8 27.3 1.0
CA C:ASP564 4.8 25.7 1.0

Magnesium binding site 4 out of 4 in 5se3

Go back to Magnesium Binding Sites List in 5se3
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Chloro-N-(2-Phenyl-[1,2,4]Triazolo[1,5-A]Pyridin-7-Yl)Pyridine-4- 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 2- Chloro-N-(2-Phenyl-[1,2,4]Triazolo[1,5-A]Pyridin-7-Yl)Pyridine-4- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:38.1
occ:1.00
 O D:HOH923 2.0 25.3 1.0
O D:HOH909 2.1 35.5 1.0
O D:HOH976 2.1 35.3 1.0
O D:HOH946 2.2 32.9 1.0
O D:HOH924 2.2 32.1 1.0
OD1 D:ASP564 2.2 35.4 1.0
CG D:ASP564 3.2 34.1 1.0
OD2 D:ASP564 3.5 46.3 1.0
O D:HOH960 3.8 38.7 1.0
ZN D:ZN801 3.8 40.6 1.0
OE2 D:GLU592 4.0 40.2 1.0
O D:HOH975 4.1 38.4 1.0
NE2 D:HIS595 4.1 42.5 1.0
OG1 D:THR633 4.2 33.7 1.0
O D:HIS563 4.3 32.9 1.0
CD2 D:HIS563 4.3 29.6 1.0
CD2 D:HIS595 4.3 37.3 1.0
CD2 D:HIS567 4.4 42.3 1.0
OD2 D:ASP674 4.4 33.2 1.0
O D:THR633 4.4 41.1 1.0
CB D:ASP564 4.5 37.4 1.0
NE2 D:HIS567 4.5 37.7 1.0
CD2 D:HIS525 4.6 38.8 1.0
CB D:THR633 4.6 33.2 1.0
NE2 D:HIS525 4.7 40.0 1.0
NE2 D:HIS563 4.8 30.5 1.0
CA D:ASP564 4.8 33.4 1.0
CG D:GLU592 4.9 40.8 1.0
CD D:GLU592 4.9 39.0 1.0
O D:HOH979 4.9 33.2 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 03:17:27 2024

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