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Fluorine in PDB 5u00: Crystal Structure of Human Phosphodiesterase 2A in Complex with 3,3- Difluoro-1-[(4-Fluoro-3-Iodophenyl)Carbonyl]-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 3,3- Difluoro-1-[(4-Fluoro-3-Iodophenyl)Carbonyl]-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 3,3- Difluoro-1-[(4-Fluoro-3-Iodophenyl)Carbonyl]-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 3,3- Difluoro-1-[(4-Fluoro-3-Iodophenyl)Carbonyl]-5-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}Piperidine, PDB code: 5u00 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) 65.53 / 1.41
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 55.986, 73.249, 91.206, 109.38, 90.79, 91.10
R / Rfree (%) 19.9 / 22.8

Other elements in 5u00:

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

Magnesium (Mg) 4 atoms
Zinc (Zn) 4 atoms
Iodine (I) 4 atoms

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Phosphodiesterase 2A in Complex with 3,3- Difluoro-1-[(4-Fluoro-3-Iodophenyl)Carbonyl]-5-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}Piperidine (pdb code 5u00). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Crystal Structure of Human Phosphodiesterase 2A in Complex with 3,3- Difluoro-1-[(4-Fluoro-3-Iodophenyl)Carbonyl]-5-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}Piperidine, PDB code: 5u00:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 5u00

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Fluorine binding site 1 out of 12 in the Crystal Structure of Human Phosphodiesterase 2A in Complex with 3,3- Difluoro-1-[(4-Fluoro-3-Iodophenyl)Carbonyl]-5-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}Piperidine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Human Phosphodiesterase 2A in Complex with 3,3- Difluoro-1-[(4-Fluoro-3-Iodophenyl)Carbonyl]-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:F1001

b:22.6
occ:1.00
 F28 A:7OV1001 0.0 22.6 1.0
C24 A:7OV1001 1.4 19.5 1.0
C23 A:7OV1001 2.3 19.8 1.0
C25 A:7OV1001 2.4 12.6 1.0
I27 A:7OV1001 3.2 18.6 1.0
C22 A:7OV1001 3.6 18.0 1.0
CB A:PHE862 3.6 20.6 1.0
C26 A:7OV1001 3.6 13.7 1.0
O A:LEU858 4.1 20.3 1.0
CA A:PHE862 4.1 18.3 1.0
C20 A:7OV1001 4.1 16.0 1.0
N A:PHE862 4.2 20.3 1.0
CD1 A:PHE862 4.2 24.2 1.0
SD A:MET847 4.3 21.8 1.0
CG A:PHE862 4.4 20.9 1.0
OG A:SER861 4.9 48.4 1.0
C A:LEU858 5.0 22.6 1.0

Fluorine binding site 2 out of 12 in 5u00

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Fluorine binding site 2 out of 12 in the Crystal Structure of Human Phosphodiesterase 2A in Complex with 3,3- Difluoro-1-[(4-Fluoro-3-Iodophenyl)Carbonyl]-5-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}Piperidine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Human Phosphodiesterase 2A in Complex with 3,3- Difluoro-1-[(4-Fluoro-3-Iodophenyl)Carbonyl]-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:F1001

b:16.4
occ:1.00
 F17 A:7OV1001 0.0 16.4 1.0
C13 A:7OV1001 1.4 14.1 1.0
F18 A:7OV1001 2.2 15.2 1.0
C12 A:7OV1001 2.3 12.1 1.0
C14 A:7OV1001 2.4 16.5 1.0
C10 A:7OV1001 2.9 10.9 1.0
N15 A:7OV1001 3.0 15.3 1.0
CZ A:PHE830 3.2 14.6 1.0
CE1 A:PHE830 3.3 14.8 1.0
C16 A:7OV1001 3.5 15.9 1.0
O A:HOH1360 3.6 16.5 1.0
C19 A:7OV1001 3.7 17.2 1.0
O A:HOH1296 3.7 24.6 1.0
CE1 A:HIS656 3.9 12.7 1.0
O21 A:7OV1001 4.0 20.5 1.0
CD1 A:ILE826 4.1 24.3 1.0
C6 A:7OV1001 4.3 10.3 1.0
NE2 A:HIS656 4.4 13.8 1.0
CE2 A:PHE830 4.5 18.6 1.0
CD1 A:PHE830 4.6 12.4 1.0
C20 A:7OV1001 4.7 16.0 1.0
O A:HOH1146 4.7 17.8 1.0
C26 A:7OV1001 4.8 13.7 1.0
O A:HOH1342 5.0 20.5 1.0

Fluorine binding site 3 out of 12 in 5u00

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Fluorine binding site 3 out of 12 in the Crystal Structure of Human Phosphodiesterase 2A in Complex with 3,3- Difluoro-1-[(4-Fluoro-3-Iodophenyl)Carbonyl]-5-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}Piperidine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Human Phosphodiesterase 2A in Complex with 3,3- Difluoro-1-[(4-Fluoro-3-Iodophenyl)Carbonyl]-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:F1001

b:15.2
occ:1.00
 F18 A:7OV1001 0.0 15.2 1.0
C13 A:7OV1001 1.4 14.1 1.0
F17 A:7OV1001 2.2 16.4 1.0
C14 A:7OV1001 2.4 16.5 1.0
C12 A:7OV1001 2.4 12.1 1.0
NE2 A:HIS656 3.1 13.8 1.0
O A:HOH1342 3.1 20.5 1.0
CE1 A:HIS656 3.1 12.7 1.0
O A:HOH1228 3.3 12.6 1.0
O A:HOH1230 3.3 16.6 1.0
N15 A:7OV1001 3.6 15.3 1.0
C10 A:7OV1001 3.7 10.9 1.0
O A:HOH1360 3.8 16.5 1.0
O A:HOH1252 4.1 13.1 1.0
C16 A:7OV1001 4.1 15.9 1.0
CD2 A:HIS656 4.4 13.7 1.0
ND1 A:HIS656 4.4 11.4 1.0
O A:HOH1219 4.6 16.5 1.0
O A:HOH1296 4.6 24.6 1.0
C19 A:7OV1001 4.6 17.2 1.0
O21 A:7OV1001 4.8 20.5 1.0
O A:HOH1260 4.9 20.9 1.0
C6 A:7OV1001 4.9 10.3 1.0

Fluorine binding site 4 out of 12 in 5u00

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Fluorine binding site 4 out of 12 in the Crystal Structure of Human Phosphodiesterase 2A in Complex with 3,3- Difluoro-1-[(4-Fluoro-3-Iodophenyl)Carbonyl]-5-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}Piperidine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Human Phosphodiesterase 2A in Complex with 3,3- Difluoro-1-[(4-Fluoro-3-Iodophenyl)Carbonyl]-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:F1001

b:21.5
occ:1.00
 F28 B:7OV1001 0.0 21.5 1.0
C24 B:7OV1001 1.4 24.9 1.0
C23 B:7OV1001 2.3 25.4 1.0
C25 B:7OV1001 2.4 20.1 1.0
I27 B:7OV1001 3.1 20.2 1.0
C22 B:7OV1001 3.6 23.0 1.0
C26 B:7OV1001 3.6 20.6 1.0
CB B:PHE862 3.8 18.7 1.0
C20 B:7OV1001 4.1 23.3 1.0
CD1 B:PHE862 4.1 21.3 1.0
O B:LEU858 4.1 21.1 1.0
SD B:MET847 4.3 24.6 1.0
CA B:PHE862 4.3 21.8 1.0
CG B:PHE862 4.4 19.6 1.0
N B:PHE862 4.5 20.4 1.0

Fluorine binding site 5 out of 12 in 5u00

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Fluorine binding site 5 out of 12 in the Crystal Structure of Human Phosphodiesterase 2A in Complex with 3,3- Difluoro-1-[(4-Fluoro-3-Iodophenyl)Carbonyl]-5-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}Piperidine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Human Phosphodiesterase 2A in Complex with 3,3- Difluoro-1-[(4-Fluoro-3-Iodophenyl)Carbonyl]-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:F1001

b:15.9
occ:1.00
 F17 B:7OV1001 0.0 15.9 1.0
C13 B:7OV1001 1.3 15.7 1.0
F18 B:7OV1001 2.1 16.2 1.0
C12 B:7OV1001 2.3 12.4 1.0
C14 B:7OV1001 2.3 15.1 1.0
N15 B:7OV1001 2.9 14.2 1.0
C10 B:7OV1001 3.0 14.3 1.0
CZ B:PHE830 3.3 16.7 1.0
CE1 B:PHE830 3.3 15.4 1.0
C16 B:7OV1001 3.5 16.7 1.0
O B:HOH1335 3.6 21.4 1.0
C19 B:7OV1001 3.7 18.4 1.0
O B:HOH1290 3.7 26.1 1.0
CE1 B:HIS656 3.8 11.8 1.0
O21 B:7OV1001 4.0 20.7 1.0
CD1 B:ILE826 4.1 31.9 1.0
C6 B:7OV1001 4.3 12.8 1.0
NE2 B:HIS656 4.3 16.1 1.0
CE2 B:PHE830 4.6 17.3 1.0
CD1 B:PHE830 4.6 14.5 1.0
O B:HOH1140 4.7 17.7 1.0
C20 B:7OV1001 4.8 23.3 1.0
C26 B:7OV1001 4.9 20.6 1.0
CG2 B:ILE826 4.9 19.8 1.0
ND1 B:HIS656 4.9 14.3 1.0
O B:HOH1251 5.0 16.9 1.0

Fluorine binding site 6 out of 12 in 5u00

Go back to Fluorine Binding Sites List in 5u00
Fluorine binding site 6 out of 12 in the Crystal Structure of Human Phosphodiesterase 2A in Complex with 3,3- Difluoro-1-[(4-Fluoro-3-Iodophenyl)Carbonyl]-5-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}Piperidine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Human Phosphodiesterase 2A in Complex with 3,3- Difluoro-1-[(4-Fluoro-3-Iodophenyl)Carbonyl]-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:F1001

b:16.2
occ:1.00
 F18 B:7OV1001 0.0 16.2 1.0
C13 B:7OV1001 1.4 15.7 1.0
F17 B:7OV1001 2.1 15.9 1.0
C14 B:7OV1001 2.3 15.1 1.0
C12 B:7OV1001 2.4 12.4 1.0
NE2 B:HIS656 3.1 16.1 1.0
O B:HOH1305 3.1 19.6 1.0
O B:HOH1251 3.1 16.9 1.0
CE1 B:HIS656 3.2 11.8 1.0
O B:HOH1234 3.3 12.6 1.0
N15 B:7OV1001 3.6 14.2 1.0
C10 B:7OV1001 3.7 14.3 1.0
O B:HOH1335 3.7 21.4 1.0
O B:HOH1270 4.0 16.0 1.0
C16 B:7OV1001 4.1 16.7 1.0
O B:HOH1318 4.1 20.3 1.0
CD2 B:HIS656 4.4 13.2 1.0
ND1 B:HIS656 4.5 14.3 1.0
C19 B:7OV1001 4.6 18.4 1.0
O B:HOH1222 4.7 17.8 1.0
O B:HOH1290 4.7 26.1 1.0
O B:HOH1255 4.7 20.3 1.0
O21 B:7OV1001 4.8 20.7 1.0
C6 B:7OV1001 4.9 12.8 1.0

Fluorine binding site 7 out of 12 in 5u00

Go back to Fluorine Binding Sites List in 5u00
Fluorine binding site 7 out of 12 in the Crystal Structure of Human Phosphodiesterase 2A in Complex with 3,3- Difluoro-1-[(4-Fluoro-3-Iodophenyl)Carbonyl]-5-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}Piperidine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of Human Phosphodiesterase 2A in Complex with 3,3- Difluoro-1-[(4-Fluoro-3-Iodophenyl)Carbonyl]-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:F1001

b:27.4
occ:1.00
 F28 C:7OV1001 0.0 27.4 1.0
C24 C:7OV1001 1.3 20.5 1.0
C25 C:7OV1001 2.3 18.9 1.0
C23 C:7OV1001 2.4 21.4 1.0
I27 C:7OV1001 3.0 19.9 1.0
O C:HOH1250 3.3 27.8 1.0
CB C:PHE862 3.5 19.5 1.0
C22 C:7OV1001 3.6 22.0 1.0
C26 C:7OV1001 3.6 17.3 1.0
O C:LEU858 3.9 22.4 1.0
SD C:MET847 4.1 27.1 1.0
C20 C:7OV1001 4.1 17.3 1.0
CA C:PHE862 4.1 19.9 1.0
CD1 C:PHE862 4.2 20.5 1.0
CG C:PHE862 4.2 19.4 1.0
N C:PHE862 4.3 18.2 1.0
C C:LEU858 4.8 21.8 1.0

Fluorine binding site 8 out of 12 in 5u00

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Fluorine binding site 8 out of 12 in the Crystal Structure of Human Phosphodiesterase 2A in Complex with 3,3- Difluoro-1-[(4-Fluoro-3-Iodophenyl)Carbonyl]-5-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}Piperidine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of Human Phosphodiesterase 2A in Complex with 3,3- Difluoro-1-[(4-Fluoro-3-Iodophenyl)Carbonyl]-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:F1001

b:18.7
occ:1.00
 F17 C:7OV1001 0.0 18.7 1.0
C13 C:7OV1001 1.4 16.7 1.0
F18 C:7OV1001 2.2 17.0 1.0
C12 C:7OV1001 2.3 15.2 1.0
C14 C:7OV1001 2.4 17.7 1.0
N15 C:7OV1001 2.9 19.0 1.0
C10 C:7OV1001 2.9 14.7 1.0
CZ C:PHE830 3.3 14.8 1.0
CE1 C:PHE830 3.4 20.7 1.0
C16 C:7OV1001 3.4 15.7 1.0
O C:HOH1317 3.7 18.8 1.0
C19 C:7OV1001 3.7 20.4 1.0
O C:HOH1287 3.8 27.6 1.0
CE1 C:HIS656 3.8 11.9 1.0
O21 C:7OV1001 4.1 19.9 1.0
CD1 C:ILE826 4.2 18.4 1.0
C6 C:7OV1001 4.2 12.8 1.0
NE2 C:HIS656 4.3 18.1 1.0
CE2 C:PHE830 4.5 19.0 1.0
O C:HOH1153 4.6 16.7 1.0
CD1 C:PHE830 4.7 18.6 1.0
C20 C:7OV1001 4.8 17.3 1.0
O C:HOH1219 4.8 19.4 1.0
C26 C:7OV1001 4.9 17.3 1.0
O C:HOH1303 4.9 22.8 1.0
CG2 C:ILE826 5.0 24.0 1.0
ND1 C:HIS656 5.0 11.7 1.0

Fluorine binding site 9 out of 12 in 5u00

Go back to Fluorine Binding Sites List in 5u00
Fluorine binding site 9 out of 12 in the Crystal Structure of Human Phosphodiesterase 2A in Complex with 3,3- Difluoro-1-[(4-Fluoro-3-Iodophenyl)Carbonyl]-5-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}Piperidine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of Human Phosphodiesterase 2A in Complex with 3,3- Difluoro-1-[(4-Fluoro-3-Iodophenyl)Carbonyl]-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:F1001

b:17.0
occ:1.00
 F18 C:7OV1001 0.0 17.0 1.0
C13 C:7OV1001 1.4 16.7 1.0
F17 C:7OV1001 2.2 18.7 1.0
C14 C:7OV1001 2.3 17.7 1.0
C12 C:7OV1001 2.4 15.2 1.0
O C:HOH1219 3.0 19.4 1.0
O C:HOH1303 3.0 22.8 1.0
NE2 C:HIS656 3.1 18.1 1.0
CE1 C:HIS656 3.2 11.9 1.0
O C:HOH1237 3.4 11.6 1.0
N15 C:7OV1001 3.6 19.0 1.0
C10 C:7OV1001 3.7 14.7 1.0
O C:HOH1306 3.7 27.0 1.0
O C:HOH1317 3.8 18.8 1.0
C16 C:7OV1001 4.2 15.7 1.0
O C:HOH1225 4.2 14.2 1.0
CD2 C:HIS656 4.4 18.0 1.0
ND1 C:HIS656 4.6 11.7 1.0
O C:HOH1170 4.6 17.1 1.0
O C:HOH1218 4.6 23.8 1.0
O C:HOH1287 4.6 27.6 1.0
C19 C:7OV1001 4.7 20.4 1.0
O21 C:7OV1001 4.8 19.9 1.0
C6 C:7OV1001 4.9 12.8 1.0

Fluorine binding site 10 out of 12 in 5u00

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Fluorine binding site 10 out of 12 in the Crystal Structure of Human Phosphodiesterase 2A in Complex with 3,3- Difluoro-1-[(4-Fluoro-3-Iodophenyl)Carbonyl]-5-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}Piperidine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of Human Phosphodiesterase 2A in Complex with 3,3- Difluoro-1-[(4-Fluoro-3-Iodophenyl)Carbonyl]-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:F1001

b:21.9
occ:1.00
 F28 D:7OV1001 0.0 21.9 1.0
C24 D:7OV1001 1.4 17.5 1.0
C23 D:7OV1001 2.4 22.8 1.0
C25 D:7OV1001 2.4 12.8 1.0
I27 D:7OV1001 3.1 18.5 1.0
O D:HOH1257 3.3 26.8 1.0
CB D:PHE862 3.6 16.8 1.0
C22 D:7OV1001 3.6 21.1 1.0
C26 D:7OV1001 3.6 13.8 1.0
CD1 D:PHE862 3.9 18.8 1.0
C20 D:7OV1001 4.1 20.8 1.0
O D:LEU858 4.1 17.0 1.0
CA D:PHE862 4.1 15.7 1.0
CG D:PHE862 4.2 18.4 1.0
SD D:MET847 4.2 21.3 1.0
N D:PHE862 4.4 17.2 1.0
CD2 D:LEU858 4.9 29.7 1.0
C D:LEU858 5.0 17.0 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: Thu Aug 1 15:28:00 2024

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