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Zinc 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
Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc 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 Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4y87

Go back to Zinc Binding Sites List in 4y87
Zinc 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 Zinc with other atoms in the Zn 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:Zn602

b:74.1
occ:1.00
 OD2 A:ASP293 2.0 54.8 1.0
OD1 A:ASP402 2.1 61.7 1.0
NE2 A:HIS292 2.2 62.9 1.0
NE2 A:HIS256 2.2 62.7 1.0
O A:HOH702 2.7 37.1 1.0
CD2 A:HIS256 3.1 58.6 1.0
CG A:ASP293 3.1 48.8 1.0
CE1 A:HIS292 3.1 58.6 1.0
CG A:ASP402 3.2 58.8 1.0
CD2 A:HIS292 3.2 56.9 1.0
CE1 A:HIS256 3.2 56.9 1.0
OD2 A:ASP402 3.6 60.5 1.0
O A:HOH701 3.7 30.9 1.0
MG A:MG603 3.8 54.3 1.0
OD1 A:ASP293 3.8 50.8 1.0
CD2 A:HIS252 4.1 53.3 1.0
NE2 A:HIS252 4.2 55.4 1.0
CB A:ASP293 4.2 47.1 1.0
CG A:HIS256 4.2 55.0 1.0
ND1 A:HIS292 4.3 54.3 1.0
ND1 A:HIS256 4.3 55.2 1.0
CG A:HIS292 4.3 52.5 1.0
CB A:ASP402 4.5 55.9 1.0
O A:HOH705 4.6 41.3 1.0
O A:ASP402 4.7 52.0 1.0
O A:HOH704 4.7 20.2 1.0
CA A:ASP402 4.8 52.3 1.0
CG2 A:VAL260 4.9 42.7 1.0

Zinc binding site 2 out of 2 in 4y87

Go back to Zinc Binding Sites List in 4y87
Zinc 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 Zinc with other atoms in the Zn 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:Zn602

b:69.4
occ:1.00
 OD2 B:ASP293 2.0 51.6 1.0
OD1 B:ASP402 2.0 59.6 1.0
NE2 B:HIS292 2.2 55.6 1.0
NE2 B:HIS256 2.2 60.0 1.0
O B:HOH701 2.7 31.1 1.0
O B:HOH702 2.8 70.6 1.0
CG B:ASP402 3.1 54.5 1.0
CE1 B:HIS292 3.1 52.7 1.0
CE1 B:HIS256 3.2 53.5 1.0
CD2 B:HIS292 3.2 51.6 1.0
CG B:ASP293 3.2 47.5 1.0
CD2 B:HIS256 3.2 57.1 1.0
OD2 B:ASP402 3.5 56.2 1.0
OD1 B:ASP293 3.8 47.1 1.0
MG B:MG603 3.9 46.9 1.0
CD2 B:HIS252 4.1 48.6 1.0
NE2 B:HIS252 4.1 51.3 1.0
ND1 B:HIS292 4.2 50.9 1.0
CB B:ASP293 4.3 46.2 1.0
ND1 B:HIS256 4.3 51.5 1.0
CG B:HIS292 4.3 50.4 1.0
CG B:HIS256 4.3 53.3 1.0
CB B:ASP402 4.4 51.8 1.0
O B:ASP402 4.4 50.9 1.0
O B:HOH703 4.4 32.3 1.0
CA B:ASP402 4.8 49.6 1.0
C B:ASP402 5.0 49.7 1.0
CG2 B:VAL260 5.0 54.1 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: Sun Oct 27 11:00:03 2024

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