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Magnesium in PDB 5up0: Crystal Structure of Human PDE1B Catalytic Domain in Complex with Inhibitor 3 (6-(4-Chlorobenzyl)-8,9,10,11-Tetrahydrobenzo[4, 5]Thieno[3,2-E][1,2,4]Triazolo[1,5-C]Pyrimidin-5(6H)-One)

Enzymatic activity of Crystal Structure of Human PDE1B Catalytic Domain in Complex with Inhibitor 3 (6-(4-Chlorobenzyl)-8,9,10,11-Tetrahydrobenzo[4, 5]Thieno[3,2-E][1,2,4]Triazolo[1,5-C]Pyrimidin-5(6H)-One)

All present enzymatic activity of Crystal Structure of Human PDE1B Catalytic Domain in Complex with Inhibitor 3 (6-(4-Chlorobenzyl)-8,9,10,11-Tetrahydrobenzo[4, 5]Thieno[3,2-E][1,2,4]Triazolo[1,5-C]Pyrimidin-5(6H)-One):
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human PDE1B Catalytic Domain in Complex with Inhibitor 3 (6-(4-Chlorobenzyl)-8,9,10,11-Tetrahydrobenzo[4, 5]Thieno[3,2-E][1,2,4]Triazolo[1,5-C]Pyrimidin-5(6H)-One), PDB code: 5up0 was solved by E.P.Cedervall, C.K.Allerston, R.Xu, V.Sridhar, R.Barker, K.Aertgeerts, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 61.79 / 2.04
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 87.381, 87.381, 135.088, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 22.6

Other elements in 5up0:

The structure of Crystal Structure of Human PDE1B Catalytic Domain in Complex with Inhibitor 3 (6-(4-Chlorobenzyl)-8,9,10,11-Tetrahydrobenzo[4, 5]Thieno[3,2-E][1,2,4]Triazolo[1,5-C]Pyrimidin-5(6H)-One) also contains other interesting chemical elements:

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

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human PDE1B Catalytic Domain in Complex with Inhibitor 3 (6-(4-Chlorobenzyl)-8,9,10,11-Tetrahydrobenzo[4, 5]Thieno[3,2-E][1,2,4]Triazolo[1,5-C]Pyrimidin-5(6H)-One) (pdb code 5up0). 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 PDE1B Catalytic Domain in Complex with Inhibitor 3 (6-(4-Chlorobenzyl)-8,9,10,11-Tetrahydrobenzo[4, 5]Thieno[3,2-E][1,2,4]Triazolo[1,5-C]Pyrimidin-5(6H)-One), PDB code: 5up0:

Magnesium binding site 1 out of 1 in 5up0

Go back to Magnesium Binding Sites List in 5up0
Magnesium binding site 1 out of 1 in the Crystal Structure of Human PDE1B Catalytic Domain in Complex with Inhibitor 3 (6-(4-Chlorobenzyl)-8,9,10,11-Tetrahydrobenzo[4, 5]Thieno[3,2-E][1,2,4]Triazolo[1,5-C]Pyrimidin-5(6H)-One)


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 PDE1B Catalytic Domain in Complex with Inhibitor 3 (6-(4-Chlorobenzyl)-8,9,10,11-Tetrahydrobenzo[4, 5]Thieno[3,2-E][1,2,4]Triazolo[1,5-C]Pyrimidin-5(6H)-One) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:26.9
occ:1.00
 O A:HOH783 1.9 28.1 1.0
O A:HOH703 2.0 31.6 1.0
O A:HOH732 2.1 29.1 1.0
O A:HOH716 2.1 27.8 1.0
OD1 A:ASP264 2.2 26.9 1.0
O A:HOH745 2.2 28.9 1.0
CG A:ASP264 3.1 32.0 1.0
OD2 A:ASP264 3.4 31.8 1.0
ZN A:ZN601 3.8 35.6 1.0
O A:HOH775 4.1 29.2 1.0
CD2 A:HIS263 4.1 26.5 1.0
NE2 A:HIS296 4.1 30.4 1.0
O A:HOH768 4.2 42.5 1.0
OG1 A:THR334 4.2 28.5 1.0
O A:HIS263 4.2 27.9 1.0
OE2 A:GLU293 4.2 33.8 1.0
CD2 A:HIS267 4.2 27.5 1.0
O A:HOH765 4.2 54.4 1.0
O A:HOH702 4.3 46.9 1.0
OD1 A:ASP370 4.4 38.8 1.0
CD2 A:HIS296 4.4 28.0 1.0
CB A:ASP264 4.5 25.8 1.0
NE2 A:HIS267 4.5 31.1 1.0
NE2 A:HIS263 4.5 28.5 1.0
NE2 A:HIS223 4.6 33.8 1.0
O A:THR334 4.7 37.2 1.0
CD2 A:HIS223 4.7 27.0 1.0
CA A:ASP264 4.8 26.7 1.0
CB A:THR334 4.9 31.3 1.0
CG A:GLU293 4.9 30.6 1.0
CD A:GLU293 5.0 32.3 1.0

Reference:

B.Dyck, B.Branstetter, T.Gharbaoui, A.R.Hudson, J.G.Breitenbucher, L.Gomez, I.Botrous, T.Marrone, R.Barido, C.K.Allerston, E.P.Cedervall, R.Xu, V.Sridhar, R.Barker, K.Aertgeerts, K.Schmelzer, D.Neul, D.Lee, M.E.Massari, C.B.Andersen, K.Sebring, X.Zhou, R.Petroski, J.Limberis, M.Augustin, L.E.Chun, T.E.Edwards, M.Peters, A.Tabatabaei. Discovery of Selective Phosphodiesterase 1 Inhibitors with Memory Enhancing Properties. J. Med. Chem. V. 60 3472 2017.
ISSN: ISSN 1520-4804
PubMed: 28406621
DOI: 10.1021/ACS.JMEDCHEM.7B00302
Page generated: Tue Aug 12 20:53:23 2025

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