Bromine 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
Magnesium (Mg) 4 atoms
Zinc (Zn) 4 atoms

Bromine Binding Sites:

The binding sites of Bromine 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 Bromine atom.
In total 4 binding sites of Bromine 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 Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in 5tzc

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Bromine 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 Bromine with other atoms in the Br 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:Br1001

b:26.8
occ:1.00
 BR24 A:7OJ1001 0.0 26.8 1.0
C21 A:7OJ1001 1.9 24.7 1.0
C27 A:7OJ1001 2.7 25.3 1.0
F28 A:7OJ1001 2.8 27.4 1.0
C20 A:7OJ1001 2.9 24.6 1.0
OH A:TYR827 3.2 21.4 1.0
C8 A:7OJ1001 3.6 19.7 1.0
OE1 A:GLN859 3.8 22.3 1.0
N9 A:7OJ1001 3.8 21.1 1.0
SD A:MET847 4.0 32.7 1.0
CZ A:TYR827 4.1 20.6 1.0
C22 A:7OJ1001 4.1 23.4 1.0
C18 A:7OJ1001 4.1 23.9 1.0
CB A:PHE862 4.2 24.6 1.0
CE2 A:PHE830 4.2 19.7 1.0
CE1 A:TYR827 4.3 21.1 1.0
O A:LEU858 4.3 25.3 1.0
CG A:PHE862 4.5 24.1 1.0
CB A:LEU858 4.5 26.8 1.0
C23 A:7OJ1001 4.6 23.8 1.0
CD1 A:PHE862 4.6 24.1 1.0
C A:LEU858 4.7 25.5 1.0
CB A:MET847 4.8 30.5 1.0
N7 A:7OJ1001 4.9 19.9 1.0
CD A:GLN859 4.9 24.3 1.0

Bromine binding site 2 out of 4 in 5tzc

Go back to Bromine Binding Sites List in 5tzc
Bromine 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 Bromine with other atoms in the Br 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:Br1001

b:34.2
occ:1.00
 BR24 B:7OJ1001 0.0 34.2 1.0
C21 B:7OJ1001 1.9 28.7 1.0
C20 B:7OJ1001 2.8 27.0 1.0
C27 B:7OJ1001 2.9 27.3 1.0
OH B:TYR827 3.1 20.9 1.0
F28 B:7OJ1001 3.2 26.8 1.0
OE1 B:GLN859 3.7 39.0 1.0
C8 B:7OJ1001 3.8 23.2 1.0
N9 B:7OJ1001 3.9 23.4 1.0
CZ B:TYR827 3.9 22.1 1.0
SD B:MET847 4.1 29.3 1.0
C18 B:7OJ1001 4.1 25.4 1.0
C22 B:7OJ1001 4.2 27.8 1.0
CB B:PHE862 4.2 28.5 1.0
CE1 B:TYR827 4.3 21.9 1.0
CE2 B:PHE830 4.3 19.6 1.0
O B:LEU858 4.3 25.4 1.0
CB B:LEU858 4.5 28.1 1.0
CG B:PHE862 4.5 30.4 1.0
C B:LEU858 4.6 27.1 1.0
CD1 B:PHE862 4.7 28.8 1.0
C23 B:7OJ1001 4.7 27.1 1.0
CD B:GLN859 4.9 30.0 1.0
CE2 B:TYR827 5.0 21.4 1.0

Bromine binding site 3 out of 4 in 5tzc

Go back to Bromine Binding Sites List in 5tzc
Bromine 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 Bromine with other atoms in the Br 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:Br1001

b:28.8
occ:1.00
 BR24 C:7OJ1001 0.0 28.8 1.0
C21 C:7OJ1001 1.9 23.9 1.0
C27 C:7OJ1001 2.8 23.1 1.0
C20 C:7OJ1001 2.9 21.3 1.0
F28 C:7OJ1001 2.9 24.2 1.0
OH C:TYR827 3.2 20.6 1.0
C8 C:7OJ1001 3.8 18.0 1.0
N9 C:7OJ1001 3.8 16.9 1.0
OE1 C:GLN859 3.8 28.7 1.0
SD C:MET847 4.0 27.3 1.0
CZ C:TYR827 4.0 20.7 1.0
C22 C:7OJ1001 4.2 20.9 1.0
CB C:PHE862 4.2 21.5 1.0
CE2 C:PHE830 4.2 21.9 1.0
C18 C:7OJ1001 4.2 21.1 1.0
CE1 C:TYR827 4.2 21.4 1.0
O C:LEU858 4.4 25.6 1.0
CG C:PHE862 4.4 21.9 1.0
CE C:MET847 4.5 31.8 1.0
CD1 C:PHE862 4.5 20.9 1.0
CB C:LEU858 4.6 28.0 1.0
C23 C:7OJ1001 4.7 21.0 1.0
C C:LEU858 4.7 27.0 1.0
CB C:MET847 4.9 26.9 1.0
CD C:GLN859 5.0 25.8 1.0
CD2 C:PHE830 5.0 21.3 1.0

Bromine binding site 4 out of 4 in 5tzc

Go back to Bromine Binding Sites List in 5tzc
Bromine 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 Bromine with other atoms in the Br 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:Br1001

b:33.5
occ:1.00
 BR24 D:7OJ1001 0.0 33.5 1.0
C21 D:7OJ1001 1.9 24.9 1.0
C27 D:7OJ1001 2.8 26.0 1.0
C20 D:7OJ1001 2.9 22.9 1.0
F28 D:7OJ1001 3.0 26.3 1.0
OH D:TYR827 3.2 20.3 1.0
C8 D:7OJ1001 3.6 18.2 1.0
N9 D:7OJ1001 3.8 17.2 1.0
OE1 D:GLN859 3.8 25.4 1.0
SD D:MET847 3.9 29.5 1.0
CZ D:TYR827 4.1 19.4 1.0
CB D:PHE862 4.1 20.7 1.0
C18 D:7OJ1001 4.2 21.4 1.0
C22 D:7OJ1001 4.2 24.2 1.0
CE2 D:PHE830 4.3 20.1 1.0
CE1 D:TYR827 4.3 19.4 1.0
CG D:PHE862 4.4 20.1 1.0
O D:LEU858 4.4 27.8 1.0
CD1 D:PHE862 4.5 21.4 1.0
CB D:LEU858 4.5 30.2 1.0
C D:LEU858 4.7 26.9 1.0
C23 D:7OJ1001 4.7 22.8 1.0
CB D:MET847 4.9 29.7 1.0
N7 D:7OJ1001 4.9 18.2 1.0
CD D:GLN859 4.9 24.6 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: Sat Dec 12 02:31:00 2020

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