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Magnesium in PDB 5see: Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-(2-Pyridin-2-Ylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino) Pyridine-2-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-(2-Pyridin-2-Ylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino) Pyridine-2-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-(2-Pyridin-2-Ylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino) Pyridine-2-Carboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-(2-Pyridin-2-Ylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino) Pyridine-2-Carboxamide, PDB code: 5see was solved by C.Joseph, R.M.Rodriguez-Sarmiento, 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) 45.22 / 2.35
Space group I 2 3
Cell size a, b, c (Å), α, β, γ (°) 142.94, 142.94, 142.94, 90, 90, 90
R / Rfree (%) 18.7 / 23.1

Other elements in 5see:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-(2-Pyridin-2-Ylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino) Pyridine-2-Carboxamide also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-(2-Pyridin-2-Ylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino) Pyridine-2-Carboxamide (pdb code 5see). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-(2-Pyridin-2-Ylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino) Pyridine-2-Carboxamide, PDB code: 5see:

Magnesium binding site 1 out of 1 in 5see

Go back to Magnesium Binding Sites List in 5see
Magnesium binding site 1 out of 1 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-(2-Pyridin-2-Ylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino) Pyridine-2-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 6- Cyclopropyl-N-(2-Pyridin-2-Ylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino) Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:48.6
occ:1.00
 O A:HOH909 2.0 43.0 1.0
O A:HOH919 2.0 51.0 1.0
O A:HOH918 2.1 41.0 1.0
OD1 A:ASP564 2.2 44.6 1.0
O A:HOH907 2.3 42.0 1.0
O A:HOH905 2.4 53.9 1.0
CG A:ASP564 3.2 41.1 1.0
OD2 A:ASP564 3.7 38.9 1.0
ZN A:ZN801 4.0 45.5 1.0
OE2 A:GLU592 4.0 43.6 1.0
NE2 A:HIS595 4.1 39.8 1.0
CD2 A:HIS567 4.2 45.9 1.0
OG1 A:THR633 4.2 46.1 1.0
OD2 A:ASP674 4.3 42.5 1.0
CD2 A:HIS563 4.3 39.5 1.0
NE2 A:HIS567 4.3 44.5 1.0
O A:THR633 4.4 41.0 1.0
CD2 A:HIS595 4.4 41.5 1.0
O A:HIS563 4.5 39.6 1.0
CB A:ASP564 4.5 40.0 1.0
CD2 A:HIS525 4.6 45.8 1.0
NE2 A:HIS525 4.6 53.3 1.0
NE2 A:HIS563 4.7 43.7 1.0
CB A:THR633 4.7 47.5 1.0
CG A:GLU592 4.8 46.9 1.0
CA A:ASP564 4.9 36.8 1.0
CD A:GLU592 4.9 47.5 1.0
O A:HOH920 4.9 42.7 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 19:19:06 2025

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