Atomistry » Chlorine » PDB 4y14-4y8c » 4y87
Atomistry »
  Chlorine »
    PDB 4y14-4y8c »
      4y87 »

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 26 03:53:30 2024

Last articles

Zn in 3HKQ
Zn in 3HKA
Zn in 3HKO
Zn in 3HKN
Zn in 3HK8
Zn in 3HK5
Zn in 3HJT
Zn in 3HJW
Zn in 3HGZ
Zn in 3HI2
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy