Chlorine in PDB 5tzx: Crystal Structure of Human Phosphodiesterase 2A in Complex with 1-[(3- Chloro-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 Phosphodiesterase 2A in Complex with 1-[(3- Chloro-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 Phosphodiesterase 2A in Complex with 1-[(3- Chloro-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 Phosphodiesterase 2A in Complex with 1-[(3- Chloro-4-Fluorophenyl)Carbonyl]-3,3-Difluoro-5-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}Piperidine, PDB code: 5tzx 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) 64.96 / 1.90
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 55.669, 72.703, 90.360, 109.28, 90.96, 90.97
R / Rfree (%) 24.8 / 30.7

Other elements in 5tzx:

The structure of Crystal Structure of Human Phosphodiesterase 2A in Complex with 1-[(3- Chloro-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

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Human Phosphodiesterase 2A in Complex with 1-[(3- Chloro-4-Fluorophenyl)Carbonyl]-3,3-Difluoro-5-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}Piperidine (pdb code 5tzx). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Human Phosphodiesterase 2A in Complex with 1-[(3- Chloro-4-Fluorophenyl)Carbonyl]-3,3-Difluoro-5-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}Piperidine, PDB code: 5tzx:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5tzx

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Chlorine binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A in Complex with 1-[(3- Chloro-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 Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Human Phosphodiesterase 2A in Complex with 1-[(3- Chloro-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:Cl1001

b:19.1
occ:1.00
CL24 A:7OY1001 0.0 19.1 1.0
C21 A:7OY1001 1.7 15.8 1.0
C27 A:7OY1001 2.6 18.7 1.0
C20 A:7OY1001 2.7 15.9 1.0
F28 A:7OY1001 2.8 25.6 1.0
OH A:TYR827 3.1 20.1 1.0
C8 A:7OY1001 3.6 10.2 1.0
N9 A:7OY1001 3.7 8.9 1.0
OE1 A:GLN859 3.9 23.4 1.0
CZ A:TYR827 3.9 19.9 1.0
C22 A:7OY1001 3.9 11.2 1.0
C18 A:7OY1001 4.0 16.2 1.0
CB A:PHE862 4.1 19.6 1.0
SD A:MET847 4.1 22.7 1.0
CE2 A:PHE830 4.2 18.2 1.0
CE1 A:TYR827 4.3 19.9 1.0
O A:LEU858 4.4 21.6 1.0
CG A:PHE862 4.4 18.8 1.0
C23 A:7OY1001 4.5 9.4 1.0
CB A:LEU858 4.5 24.1 1.0
CD1 A:PHE862 4.7 18.4 1.0
C A:LEU858 4.7 22.0 1.0
CE2 A:TYR827 4.9 19.7 1.0
N7 A:7OY1001 4.9 20.4 1.0
CB A:MET847 4.9 21.2 1.0

Chlorine binding site 2 out of 4 in 5tzx

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Chlorine binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A in Complex with 1-[(3- Chloro-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 Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Human Phosphodiesterase 2A in Complex with 1-[(3- Chloro-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:Cl1001

b:23.0
occ:1.00
CL24 B:7OY1001 0.0 23.0 1.0
C21 B:7OY1001 1.7 15.1 1.0
C20 B:7OY1001 2.7 12.1 1.0
C27 B:7OY1001 2.7 13.8 1.0
F28 B:7OY1001 2.9 15.4 1.0
OH B:TYR827 3.0 17.5 1.0
N9 B:7OY1001 3.6 14.7 1.0
OE1 B:GLN859 3.7 16.7 1.0
C8 B:7OY1001 3.7 19.0 1.0
CZ B:TYR827 3.8 17.5 1.0
C18 B:7OY1001 3.9 18.6 1.0
C22 B:7OY1001 4.0 23.0 1.0
SD B:MET847 4.0 16.9 1.0
CB B:PHE862 4.1 16.7 1.0
O B:LEU858 4.2 18.7 1.0
CE1 B:TYR827 4.2 17.7 1.0
CE2 B:PHE830 4.2 15.5 1.0
CG B:PHE862 4.4 23.4 1.0
C23 B:7OY1001 4.5 17.0 1.0
CB B:LEU858 4.6 26.8 1.0
C B:LEU858 4.6 23.4 1.0
CD1 B:PHE862 4.8 18.5 1.0
CE2 B:TYR827 4.8 17.2 1.0
CD B:GLN859 4.9 17.2 1.0
N5 B:7OY1001 5.0 15.9 1.0

Chlorine binding site 3 out of 4 in 5tzx

Go back to Chlorine Binding Sites List in 5tzx
Chlorine binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A in Complex with 1-[(3- Chloro-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 Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Human Phosphodiesterase 2A in Complex with 1-[(3- Chloro-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:Cl1001

b:21.4
occ:1.00
CL24 C:7OY1001 0.0 21.4 1.0
C21 C:7OY1001 1.7 24.4 1.0
C20 C:7OY1001 2.7 23.7 1.0
C27 C:7OY1001 2.7 22.0 1.0
F28 C:7OY1001 2.9 30.6 1.0
OH C:TYR827 3.1 25.7 1.0
N9 C:7OY1001 3.5 15.4 1.0
C8 C:7OY1001 3.5 18.6 1.0
CZ C:TYR827 3.8 25.5 1.0
OE1 C:GLN859 3.9 23.9 1.0
C18 C:7OY1001 3.9 20.4 1.0
CE2 C:PHE830 3.9 31.7 1.0
SD C:MET847 3.9 30.7 1.0
C22 C:7OY1001 4.0 20.9 1.0
CE1 C:TYR827 4.0 26.1 1.0
O C:LEU858 4.3 27.5 1.0
CB C:PHE862 4.3 24.3 1.0
C23 C:7OY1001 4.5 16.8 1.0
CG C:PHE862 4.5 22.8 1.0
CD2 C:PHE830 4.7 24.0 1.0
CD1 C:PHE862 4.7 22.4 1.0
CB C:LEU858 4.7 29.4 1.0
C C:LEU858 4.7 29.3 1.0
N5 C:7OY1001 4.8 10.8 1.0
CE C:MET847 4.8 31.4 1.0
CE2 C:TYR827 4.8 24.9 1.0
CZ C:PHE830 4.8 21.9 1.0
N7 C:7OY1001 4.8 19.4 1.0
CB C:MET847 4.9 32.8 1.0
CG C:MET847 5.0 27.5 1.0

Chlorine binding site 4 out of 4 in 5tzx

Go back to Chlorine Binding Sites List in 5tzx
Chlorine binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A in Complex with 1-[(3- Chloro-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 Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Human Phosphodiesterase 2A in Complex with 1-[(3- Chloro-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:Cl1001

b:17.8
occ:1.00
CL24 D:7OY1001 0.0 17.8 1.0
C21 D:7OY1001 1.7 15.4 1.0
C27 D:7OY1001 2.6 21.9 1.0
C20 D:7OY1001 2.7 12.5 1.0
F28 D:7OY1001 2.8 17.5 1.0
OH D:TYR827 3.3 18.1 1.0
C8 D:7OY1001 3.5 13.4 1.0
N9 D:7OY1001 3.6 15.3 1.0
SD D:MET847 3.7 18.9 1.0
OE1 D:GLN859 3.8 29.0 1.0
C22 D:7OY1001 3.9 21.6 1.0
C18 D:7OY1001 4.0 13.0 1.0
CB D:PHE862 4.1 17.4 1.0
CZ D:TYR827 4.1 18.2 1.0
CE D:MET847 4.1 17.4 1.0
CE2 D:PHE830 4.2 20.7 1.0
CG D:PHE862 4.3 17.0 1.0
CD1 D:PHE862 4.3 16.7 1.0
O D:LEU858 4.4 19.1 1.0
CE1 D:TYR827 4.5 18.1 1.0
C23 D:7OY1001 4.5 14.2 1.0
CB D:LEU858 4.6 18.8 1.0
C D:LEU858 4.7 18.8 1.0
N7 D:7OY1001 4.8 19.4 1.0
CB D:MET847 4.8 20.6 1.0
N5 D:7OY1001 4.9 16.6 1.0
CE2 D:TYR827 5.0 18.4 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 12:29:50 2020

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