Magnesium in PDB 5tzc: Crystal Structure of Human PDE2A in Complex with (5S)-1-[(3-Bromo-4- Fluorophenyl)Carbonyl]-3,3-Difluoro-5-{5-Methyl-[1,2,4]Triazolo[1,5- A]Pyrimidin-7-Yl}Piperidine

Enzymatic activity of Crystal Structure of Human PDE2A in Complex with (5S)-1-[(3-Bromo-4- Fluorophenyl)Carbonyl]-3,3-Difluoro-5-{5-Methyl-[1,2,4]Triazolo[1,5- A]Pyrimidin-7-Yl}Piperidine

All present enzymatic activity of Crystal Structure of Human PDE2A in Complex with (5S)-1-[(3-Bromo-4- Fluorophenyl)Carbonyl]-3,3-Difluoro-5-{5-Methyl-[1,2,4]Triazolo[1,5- A]Pyrimidin-7-Yl}Piperidine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human PDE2A in Complex with (5S)-1-[(3-Bromo-4- Fluorophenyl)Carbonyl]-3,3-Difluoro-5-{5-Methyl-[1,2,4]Triazolo[1,5- A]Pyrimidin-7-Yl}Piperidine, PDB code: 5tzc was solved by R.Xu, K.Aertgeerts, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.81 / 2.36
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 55.850, 73.437, 91.322, 109.60, 90.90, 91.24
R / Rfree (%) 20.1 / 24

Other elements in 5tzc:

The structure of Crystal Structure of Human PDE2A in Complex with (5S)-1-[(3-Bromo-4- Fluorophenyl)Carbonyl]-3,3-Difluoro-5-{5-Methyl-[1,2,4]Triazolo[1,5- A]Pyrimidin-7-Yl}Piperidine also contains other interesting chemical elements:

Fluorine (F) 12 atoms
Zinc (Zn) 4 atoms
Bromine (Br) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human PDE2A in Complex with (5S)-1-[(3-Bromo-4- Fluorophenyl)Carbonyl]-3,3-Difluoro-5-{5-Methyl-[1,2,4]Triazolo[1,5- A]Pyrimidin-7-Yl}Piperidine (pdb code 5tzc). 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 PDE2A in Complex with (5S)-1-[(3-Bromo-4- Fluorophenyl)Carbonyl]-3,3-Difluoro-5-{5-Methyl-[1,2,4]Triazolo[1,5- A]Pyrimidin-7-Yl}Piperidine, PDB code: 5tzc:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5tzc

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Magnesium binding site 1 out of 4 in the Crystal Structure of Human PDE2A in Complex with (5S)-1-[(3-Bromo-4- Fluorophenyl)Carbonyl]-3,3-Difluoro-5-{5-Methyl-[1,2,4]Triazolo[1,5- A]Pyrimidin-7-Yl}Piperidine


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 PDE2A in Complex with (5S)-1-[(3-Bromo-4- Fluorophenyl)Carbonyl]-3,3-Difluoro-5-{5-Methyl-[1,2,4]Triazolo[1,5- A]Pyrimidin-7-Yl}Piperidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1003

b:15.9
occ:1.00
O A:HOH1122 1.8 11.5 1.0
O A:HOH1132 2.0 5.3 1.0
OD1 A:ASP697 2.0 16.3 1.0
O A:HOH1112 2.1 10.8 1.0
O A:HOH1129 2.1 5.4 1.0
O A:HOH1115 2.2 8.3 1.0
CG A:ASP697 3.0 16.9 1.0
OD2 A:ASP697 3.2 17.7 1.0
ZN A:ZN1002 3.7 22.1 1.0
O A:HOH1128 4.0 13.3 1.0
NE2 A:HIS730 4.0 18.5 1.0
CD2 A:HIS696 4.1 17.9 1.0
O A:HIS696 4.2 17.4 1.0
OG1 A:THR768 4.2 15.4 1.0
OE2 A:GLU727 4.2 14.8 1.0
CD2 A:HIS730 4.3 18.4 1.0
NE2 A:HIS656 4.3 28.5 1.0
CB A:ASP697 4.3 15.9 1.0
CD2 A:HIS700 4.4 16.1 1.0
CD2 A:HIS656 4.5 26.7 1.0
OD2 A:ASP808 4.5 16.6 1.0
NE2 A:HIS696 4.5 19.1 1.0
CB A:THR768 4.7 17.3 1.0
NE2 A:HIS700 4.7 15.7 1.0
CA A:ASP697 4.7 16.2 1.0
O A:THR768 4.8 17.0 1.0
C A:HIS696 5.0 16.1 1.0

Magnesium binding site 2 out of 4 in 5tzc

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Magnesium binding site 2 out of 4 in the Crystal Structure of Human PDE2A in Complex with (5S)-1-[(3-Bromo-4- Fluorophenyl)Carbonyl]-3,3-Difluoro-5-{5-Methyl-[1,2,4]Triazolo[1,5- A]Pyrimidin-7-Yl}Piperidine


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 PDE2A in Complex with (5S)-1-[(3-Bromo-4- Fluorophenyl)Carbonyl]-3,3-Difluoro-5-{5-Methyl-[1,2,4]Triazolo[1,5- A]Pyrimidin-7-Yl}Piperidine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1003

b:10.6
occ:1.00
OD1 B:ASP697 2.0 19.1 1.0
O B:HOH1103 2.1 13.7 1.0
O B:HOH1130 2.1 10.5 1.0
O B:HOH1102 2.2 10.0 1.0
O B:HOH1105 2.2 15.8 1.0
O B:HOH1122 2.2 10.6 1.0
CG B:ASP697 3.0 19.3 1.0
OD2 B:ASP697 3.3 18.8 1.0
ZN B:ZN1002 3.7 24.1 1.0
O B:HOH1135 4.0 21.0 1.0
OE2 B:GLU727 4.0 20.1 1.0
NE2 B:HIS730 4.0 16.4 1.0
OG1 B:THR768 4.0 15.5 1.0
CD2 B:HIS696 4.1 17.0 1.0
O B:HIS696 4.1 18.5 1.0
CD2 B:HIS730 4.3 16.3 1.0
CB B:ASP697 4.4 19.2 1.0
NE2 B:HIS656 4.5 18.3 1.0
CD2 B:HIS700 4.5 21.3 1.0
OD2 B:ASP808 4.5 17.7 1.0
NE2 B:HIS696 4.5 18.4 1.0
CB B:THR768 4.5 16.4 1.0
CD2 B:HIS656 4.6 17.9 1.0
CA B:ASP697 4.7 18.9 1.0
NE2 B:HIS700 4.7 21.7 1.0
O B:THR768 4.8 17.4 1.0
CD B:GLU727 4.9 20.6 1.0
CG B:GLU727 4.9 19.8 1.0
C B:HIS696 4.9 17.5 1.0

Magnesium binding site 3 out of 4 in 5tzc

Go back to Magnesium Binding Sites List in 5tzc
Magnesium binding site 3 out of 4 in the Crystal Structure of Human PDE2A in Complex with (5S)-1-[(3-Bromo-4- Fluorophenyl)Carbonyl]-3,3-Difluoro-5-{5-Methyl-[1,2,4]Triazolo[1,5- A]Pyrimidin-7-Yl}Piperidine


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 PDE2A in Complex with (5S)-1-[(3-Bromo-4- Fluorophenyl)Carbonyl]-3,3-Difluoro-5-{5-Methyl-[1,2,4]Triazolo[1,5- A]Pyrimidin-7-Yl}Piperidine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1003

b:10.5
occ:1.00
O C:HOH1102 1.9 8.7 1.0
O C:HOH1128 2.0 2.9 1.0
OD1 C:ASP697 2.1 20.7 1.0
O C:HOH1101 2.1 7.6 1.0
O C:HOH1120 2.3 4.4 1.0
O C:HOH1108 2.3 12.9 1.0
CG C:ASP697 2.9 21.5 1.0
OD2 C:ASP697 3.1 19.9 1.0
ZN C:ZN1002 3.4 23.6 1.0
O C:HOH1117 3.4 16.3 1.0
O C:HOH1133 3.9 8.3 1.0
CD2 C:HIS696 4.0 20.2 1.0
NE2 C:HIS656 4.2 23.9 1.0
OD2 C:ASP808 4.3 17.0 1.0
OG1 C:THR768 4.3 13.8 1.0
NE2 C:HIS730 4.3 18.1 1.0
CD2 C:HIS656 4.3 22.7 1.0
OE2 C:GLU727 4.3 15.4 1.0
O C:HIS696 4.3 18.8 1.0
CB C:ASP697 4.4 20.6 1.0
NE2 C:HIS696 4.4 18.8 1.0
CD2 C:HIS700 4.5 21.6 1.0
CB C:THR768 4.6 14.4 1.0
CD2 C:HIS730 4.6 17.3 1.0
NE2 C:HIS700 4.7 22.5 1.0
O C:THR768 4.7 16.3 1.0
CA C:ASP697 4.8 20.7 1.0
F26 C:7OJ1001 4.9 20.6 1.0

Magnesium binding site 4 out of 4 in 5tzc

Go back to Magnesium Binding Sites List in 5tzc
Magnesium binding site 4 out of 4 in the Crystal Structure of Human PDE2A in Complex with (5S)-1-[(3-Bromo-4- Fluorophenyl)Carbonyl]-3,3-Difluoro-5-{5-Methyl-[1,2,4]Triazolo[1,5- A]Pyrimidin-7-Yl}Piperidine


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 PDE2A in Complex with (5S)-1-[(3-Bromo-4- Fluorophenyl)Carbonyl]-3,3-Difluoro-5-{5-Methyl-[1,2,4]Triazolo[1,5- A]Pyrimidin-7-Yl}Piperidine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1003

b:4.8
occ:1.00
OD1 D:ASP697 2.0 13.8 1.0
O D:HOH1110 2.0 12.2 1.0
O D:HOH1112 2.1 7.2 1.0
O D:HOH1102 2.1 3.5 1.0
O D:HOH1130 2.1 14.9 1.0
O D:HOH1111 2.2 14.5 1.0
CG D:ASP697 2.9 15.1 1.0
OD2 D:ASP697 3.2 13.9 1.0
ZN D:ZN1002 3.7 23.2 1.0
O D:HOH1114 3.9 12.3 1.0
CD2 D:HIS696 4.0 17.1 1.0
OG1 D:THR768 4.1 12.2 1.0
NE2 D:HIS730 4.1 14.6 1.0
O D:HIS696 4.1 15.7 1.0
OE2 D:GLU727 4.1 15.7 1.0
CB D:ASP697 4.3 16.0 1.0
CD2 D:HIS730 4.4 14.1 1.0
OD2 D:ASP808 4.4 15.1 1.0
NE2 D:HIS656 4.4 17.7 1.0
NE2 D:HIS696 4.4 17.5 1.0
CB D:THR768 4.5 13.1 1.0
CD2 D:HIS700 4.5 20.6 1.0
CD2 D:HIS656 4.6 17.6 1.0
O D:THR768 4.7 14.2 1.0
CA D:ASP697 4.7 16.7 1.0
NE2 D:HIS700 4.7 19.9 1.0
C D:HIS696 4.9 16.6 1.0
CD D:GLU727 5.0 16.0 1.0

Reference:

L.Gomez, M.E.Massari, T.Vickers, G.Freestone, W.Vernier, K.Ly, R.Xu, M.Mccarrick, T.Marrone, M.Metz, Y.G.Yan, Z.W.Yoder, R.Lemus, N.J.Broadbent, R.Barido, N.Warren, K.Schmelzer, D.Neul, D.Lee, C.B.Andersen, K.Sebring, K.Aertgeerts, X.Zhou, A.Tabatabaei, M.Peters, J.G.Breitenbucher. Design and Synthesis of Novel and Selective Phosphodiesterase 2 (PDE2A) Inhibitors For the Treatment of Memory Disorders. J. Med. Chem. V. 60 2037 2017.
ISSN: ISSN 1520-4804
PubMed: 28165743
DOI: 10.1021/ACS.JMEDCHEM.6B01793
Page generated: Mon Dec 14 21:13:34 2020

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