Magnesium in PDB 8syc: Crystal Structure of PDE3B in Complex with GSK4394835A

All present enzymatic activity of Crystal Structure of PDE3B in Complex with GSK4394835A:
3.1.4.17;

The structure of Crystal Structure of PDE3B in Complex with GSK4394835A, PDB code: 8syc was solved by N.O.Concha, R.Nolte, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	71.16 / 2.70
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	78.586, 78.586, 166.339, 90, 90, 90
R / Rfree (%)	17.7 / 22.4

The binding sites of Magnesium atom in the Crystal Structure of PDE3B in Complex with GSK4394835A (pdb code 8syc). 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 PDE3B in Complex with GSK4394835A, PDB code: 8syc:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of PDE3B in Complex with GSK4394835A


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 PDE3B in Complex with GSK4394835A within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1101 b:23.3 occ:1.00 O A:HOH1203 1.6 26.6 1.0 NE2 A:HIS741 2.0 42.0 1.0 OD2 A:ASP822 2.0 33.5 1.0 OD1 A:ASP937 2.1 31.7 1.0 NE2 A:HIS821 2.4 40.9 1.0 O A:HOH1218 2.6 37.6 1.0 CG A:ASP937 3.0 35.0 1.0 CD2 A:HIS741 3.0 41.9 1.0 CE1 A:HIS741 3.0 44.7 1.0 CG A:ASP822 3.1 35.8 1.0 OD2 A:ASP937 3.2 38.8 1.0 CD2 A:HIS821 3.2 38.6 1.0 CE1 A:HIS821 3.4 38.9 1.0 MG A:MG1102 3.6 40.9 1.0 OD1 A:ASP822 3.6 38.2 1.0 O A:HOH1206 3.9 39.6 1.0 CD2 A:HIS737 4.1 55.4 1.0 ND1 A:HIS741 4.1 42.3 1.0 CG A:HIS741 4.1 42.9 1.0 O36 A:X5W1103 4.2 95.3 1.0 CG A:HIS821 4.4 36.6 1.0 CB A:ASP937 4.4 35.3 1.0 CB A:ASP822 4.4 36.4 1.0 ND1 A:HIS821 4.5 36.9 1.0 NE2 A:HIS737 4.5 60.4 1.0 O A:HOH1219 4.5 61.7 1.0 O A:ASP937 4.6 35.8 1.0 CE2 A:TYR736 4.8 45.5 1.0 O A:HOH1209 4.8 41.1 1.0 CG2 A:VAL745 4.8 49.2 1.0 CA A:ASP937 4.9 35.5 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of PDE3B in Complex with GSK4394835A


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 PDE3B in Complex with GSK4394835A within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1102 b:40.9 occ:1.00 O A:HOH1222 2.0 33.1 1.0 O A:HOH1203 2.1 26.6 1.0 O A:HOH1219 2.2 61.7 1.0 OD1 A:ASP822 2.2 38.2 1.0 O36 A:X5W1103 2.5 95.3 1.0 O A:HOH1209 2.5 41.1 1.0 B35 A:X5W1103 3.1 97.3 1.0 CG A:ASP822 3.1 35.8 1.0 O A:HOH1218 3.3 37.6 1.0 O37 A:X5W1103 3.3 80.6 1.0 OD2 A:ASP822 3.4 33.5 1.0 MG A:MG1101 3.6 23.3 1.0 CD2 A:HIS737 4.0 55.4 1.0 OE2 A:GLU851 4.0 43.6 1.0 NE2 A:HIS737 4.1 60.4 1.0 NE2 A:HIS854 4.2 35.8 1.0 OD2 A:ASP937 4.2 38.8 1.0 CD2 A:HIS825 4.3 38.0 1.0 C20 A:X5W1103 4.3 105.8 1.0 CD2 A:HIS821 4.4 38.6 1.0 CD2 A:HIS854 4.5 34.9 1.0 O A:HIS821 4.5 39.2 1.0 CB A:ASP822 4.5 36.4 1.0 OG1 A:THR893 4.6 39.3 1.0 NE2 A:HIS825 4.6 37.8 1.0 NE2 A:HIS821 4.6 40.9 1.0 C19 A:X5W1103 4.9 96.3 1.0 O A:THR893 4.9 34.5 1.0 OD1 A:ASP937 4.9 31.7 1.0 CA A:ASP822 5.0 37.8 1.0 CD A:GLU851 5.0 42.1 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of PDE3B in Complex with GSK4394835A


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 PDE3B in Complex with GSK4394835A within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1101 b:32.5 occ:1.00 O D:HOH1205 1.5 36.2 1.0 O37 D:X5W1103 2.1 50.6 1.0 OD1 D:ASP937 2.2 42.4 1.0 OD2 D:ASP822 2.3 33.4 1.0 NE2 D:HIS741 2.3 41.6 1.0 NE2 D:HIS821 2.9 36.3 1.0 CG D:ASP937 3.0 42.7 1.0 OD2 D:ASP937 3.2 41.6 1.0 O D:HOH1224 3.2 35.8 1.0 MG D:MG1102 3.2 36.2 1.0 CG D:ASP822 3.3 32.9 1.0 CE1 D:HIS741 3.3 43.1 1.0 CD2 D:HIS741 3.3 45.0 1.0 B35 D:X5W1103 3.4 49.7 1.0 OD1 D:ASP822 3.6 30.1 1.0 CD2 D:HIS821 3.6 36.8 1.0 CD2 D:HIS737 3.9 35.7 1.0 CE1 D:HIS821 4.0 38.4 1.0 O36 D:X5W1103 4.0 47.0 1.0 NE2 D:HIS737 4.1 34.7 1.0 O D:HOH1218 4.2 38.8 1.0 ND1 D:HIS741 4.4 43.1 1.0 CG D:HIS741 4.4 44.6 1.0 CE2 D:TYR736 4.4 41.2 1.0 CB D:ASP937 4.5 43.4 1.0 O D:ASP937 4.5 38.7 1.0 O D:HOH1222 4.5 23.7 1.0 C20 D:X5W1103 4.5 51.6 1.0 C19 D:X5W1103 4.5 51.3 1.0 O D:HOH1212 4.6 19.0 1.0 CB D:ASP822 4.6 33.8 1.0 OH D:TYR736 4.8 38.2 1.0 CG D:HIS821 4.9 34.9 1.0 CA D:ASP937 5.0 40.4 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of PDE3B in Complex with GSK4394835A


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 PDE3B in Complex with GSK4394835A within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1102 b:36.2 occ:1.00 O D:HOH1208 2.0 33.7 1.0 O D:HOH1222 2.0 23.7 1.0 OD1 D:ASP822 2.0 30.1 1.0 O36 D:X5W1103 2.1 47.0 1.0 O D:HOH1205 2.2 36.2 1.0 O D:HOH1212 2.2 19.0 1.0 B35 D:X5W1103 2.8 49.7 1.0 O37 D:X5W1103 2.8 50.6 1.0 CG D:ASP822 3.0 32.9 1.0 MG D:MG1101 3.2 32.5 1.0 OD2 D:ASP822 3.3 33.4 1.0 CD2 D:HIS737 4.1 35.7 1.0 CD2 D:HIS821 4.2 36.8 1.0 NE2 D:HIS854 4.2 33.0 1.0 C20 D:X5W1103 4.2 51.6 1.0 OE2 D:GLU851 4.2 37.8 1.0 NE2 D:HIS737 4.3 34.7 1.0 O D:HIS821 4.3 29.8 1.0 OD2 D:ASP937 4.3 41.6 1.0 CB D:ASP822 4.3 33.8 1.0 CD2 D:HIS854 4.4 33.5 1.0 CD2 D:HIS825 4.4 33.4 1.0 OG1 D:THR893 4.4 30.5 1.0 O D:HOH1218 4.4 38.8 1.0 NE2 D:HIS821 4.5 36.3 1.0 NE2 D:HIS825 4.7 33.3 1.0 CA D:ASP822 4.8 33.6 1.0 OD1 D:ASP937 4.8 42.4 1.0 CB D:THR893 4.9 31.4 1.0 CG D:ASP937 5.0 42.7 1.0 C21 D:X5W1103 5.0 55.2 1.0

A.M.Rowley, G.Yao, L.Andrews, A.Bedermann, R.Biddulph, R.Bingham, J.J.Brady, R.Buxton, T.Cecconie, R.Cooper, A.Csakai, E.N.Gao, M.C.Grenier-Davies, M.Lawler, Y.Lian, J.Macina, C.Macphee, L.Marcaurelle, J.Martin, P.Mccormick, R.Pindoria, M.Rauch, W.Rocque, Y.Shen, L.M.Shewchuk, M.Squire, W.Stebbeds, W.Tear, X.Wang, P.Ward, S.Xiao. Discovery and Sar Study of Boronic Acid-Based Selective PDE3B Inhibitors From A Novel Dna-Encoded Library. J.Med.Chem. 2024.
ISSN: ISSN 0022-2623
PubMed: 38284310
DOI: 10.1021/ACS.JMEDCHEM.3C01562