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Chlorine in PDB 4y87: Crystal Structure of Phosphodiesterase 9 in Complex with (R)-C33 (6- {[(1R)-1-(4-Chlorophenyl)Ethyl]Amino}-1-Cyclopentyl-1,5-Dihydro-4H- Pyrazolo[3,4-D]Pyrimidin-4-One)

Enzymatic activity of Crystal Structure of Phosphodiesterase 9 in Complex with (R)-C33 (6- {[(1R)-1-(4-Chlorophenyl)Ethyl]Amino}-1-Cyclopentyl-1,5-Dihydro-4H- Pyrazolo[3,4-D]Pyrimidin-4-One)

All present enzymatic activity of Crystal Structure of Phosphodiesterase 9 in Complex with (R)-C33 (6- {[(1R)-1-(4-Chlorophenyl)Ethyl]Amino}-1-Cyclopentyl-1,5-Dihydro-4H- Pyrazolo[3,4-D]Pyrimidin-4-One):
3.1.4.35;

Protein crystallography data

The structure of Crystal Structure of Phosphodiesterase 9 in Complex with (R)-C33 (6- {[(1R)-1-(4-Chlorophenyl)Ethyl]Amino}-1-Cyclopentyl-1,5-Dihydro-4H- Pyrazolo[3,4-D]Pyrimidin-4-One), PDB code: 4y87 was solved by M.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 98.22 / 3.10
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 105.436, 105.436, 270.056, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 24.7

Other elements in 4y87:

The structure of Crystal Structure of Phosphodiesterase 9 in Complex with (R)-C33 (6- {[(1R)-1-(4-Chlorophenyl)Ethyl]Amino}-1-Cyclopentyl-1,5-Dihydro-4H- Pyrazolo[3,4-D]Pyrimidin-4-One) also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Zinc (Zn) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Phosphodiesterase 9 in Complex with (R)-C33 (6- {[(1R)-1-(4-Chlorophenyl)Ethyl]Amino}-1-Cyclopentyl-1,5-Dihydro-4H- Pyrazolo[3,4-D]Pyrimidin-4-One) (pdb code 4y87). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of Phosphodiesterase 9 in Complex with (R)-C33 (6- {[(1R)-1-(4-Chlorophenyl)Ethyl]Amino}-1-Cyclopentyl-1,5-Dihydro-4H- Pyrazolo[3,4-D]Pyrimidin-4-One), PDB code: 4y87:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 4y87

Go back to Chlorine Binding Sites List in 4y87
Chlorine binding site 1 out of 2 in the Crystal Structure of Phosphodiesterase 9 in Complex with (R)-C33 (6- {[(1R)-1-(4-Chlorophenyl)Ethyl]Amino}-1-Cyclopentyl-1,5-Dihydro-4H- Pyrazolo[3,4-D]Pyrimidin-4-One)


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 Phosphodiesterase 9 in Complex with (R)-C33 (6- {[(1R)-1-(4-Chlorophenyl)Ethyl]Amino}-1-Cyclopentyl-1,5-Dihydro-4H- Pyrazolo[3,4-D]Pyrimidin-4-One) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl601

b:0.7
occ:1.00
 CL A:49E601 0.0 0.7 1.0
C27 A:49E601 1.7 87.2 1.0
C28 A:49E601 2.6 80.9 1.0
C26 A:49E601 2.7 84.3 1.0
C29 A:49E601 3.9 77.5 1.0
C25 A:49E601 3.9 82.2 1.0
CG2 A:VAL460 4.4 50.3 1.0
C24 A:49E601 4.4 75.7 1.0
CD1 A:PHE456 4.6 51.5 1.0

Chlorine binding site 2 out of 2 in 4y87

Go back to Chlorine Binding Sites List in 4y87
Chlorine binding site 2 out of 2 in the Crystal Structure of Phosphodiesterase 9 in Complex with (R)-C33 (6- {[(1R)-1-(4-Chlorophenyl)Ethyl]Amino}-1-Cyclopentyl-1,5-Dihydro-4H- Pyrazolo[3,4-D]Pyrimidin-4-One)


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 Phosphodiesterase 9 in Complex with (R)-C33 (6- {[(1R)-1-(4-Chlorophenyl)Ethyl]Amino}-1-Cyclopentyl-1,5-Dihydro-4H- Pyrazolo[3,4-D]Pyrimidin-4-One) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl601

b:67.7
occ:1.00
 CL B:49E601 0.0 67.7 1.0
C27 B:49E601 1.7 60.6 1.0
C28 B:49E601 2.7 60.3 1.0
C26 B:49E601 2.7 58.7 1.0
C29 B:49E601 4.0 59.0 1.0
C25 B:49E601 4.0 58.4 1.0
C24 B:49E601 4.5 57.5 1.0
CD1 B:PHE456 4.7 54.0 1.0
CG2 B:VAL460 4.9 53.2 1.0

Reference:

M.Huang, Y.Shao, J.Hou, W.Cui, B.Liang, Y.Huang, Z.Li, Y.Wu, X.Zhu, P.Liu, Y.Wan, H.Ke, H.B.Luo. Structural Asymmetry of Phosphodiesterase-9A and A Unique Pocket For Selective Binding of A Potent Enantiomeric Inhibitor. Mol.Pharmacol. V. 88 836 2015.
ISSN: ESSN 1521-0111
PubMed: 26316540
DOI: 10.1124/MOL.115.099747
Page generated: Fri Jul 11 23:13:29 2025

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