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Zinc in PDB 3jsi: Human Phosphodiesterase 9 in Complex with Inhibitor

Enzymatic activity of Human Phosphodiesterase 9 in Complex with Inhibitor

All present enzymatic activity of Human Phosphodiesterase 9 in Complex with Inhibitor:
3.1.4.35;

Protein crystallography data

The structure of Human Phosphodiesterase 9 in Complex with Inhibitor, PDB code: 3jsi was solved by S.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.65 / 2.72
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 104.099, 104.099, 271.040, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 21.8

Other elements in 3jsi:

The structure of Human Phosphodiesterase 9 in Complex with Inhibitor also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Human Phosphodiesterase 9 in Complex with Inhibitor (pdb code 3jsi). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Human Phosphodiesterase 9 in Complex with Inhibitor, PDB code: 3jsi:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3jsi

Go back to Zinc Binding Sites List in 3jsi
Zinc binding site 1 out of 2 in the Human Phosphodiesterase 9 in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Phosphodiesterase 9 in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn901

b:79.2
occ:1.00
OD1 A:ASP402 2.1 53.9 1.0
OD2 A:ASP293 2.1 49.4 1.0
NE2 A:HIS256 2.5 45.0 1.0
NE2 A:HIS292 2.5 39.9 1.0
CD2 A:HIS292 3.1 40.0 1.0
CG A:ASP402 3.1 53.0 1.0
CG A:ASP293 3.2 44.3 1.0
CE1 A:HIS256 3.3 44.9 1.0
OD2 A:ASP402 3.5 59.6 1.0
O A:HOH951 3.5 48.0 1.0
CD2 A:HIS256 3.5 45.3 1.0
OD1 A:ASP293 3.6 45.0 1.0
MG A:MG902 3.7 76.9 1.0
CE1 A:HIS292 3.7 39.5 1.0
CD2 A:HIS252 3.9 41.1 1.0
NE2 A:HIS252 4.0 41.0 1.0
CG A:HIS292 4.4 38.1 1.0
O A:ASP402 4.4 45.4 1.0
CB A:ASP402 4.5 41.6 1.0
CB A:ASP293 4.5 34.9 1.0
ND1 A:HIS256 4.5 45.6 1.0
O A:HOH954 4.6 42.6 1.0
CG A:HIS256 4.6 43.8 1.0
ND1 A:HIS292 4.7 39.9 1.0
CA A:ASP402 4.8 40.0 1.0
O A:HOH952 4.9 41.4 1.0

Zinc binding site 2 out of 2 in 3jsi

Go back to Zinc Binding Sites List in 3jsi
Zinc binding site 2 out of 2 in the Human Phosphodiesterase 9 in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Phosphodiesterase 9 in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn901

b:77.1
occ:1.00
OD1 B:ASP402 2.1 55.4 1.0
OD2 B:ASP293 2.1 52.8 1.0
NE2 B:HIS256 2.5 49.7 1.0
NE2 B:HIS292 2.5 46.3 1.0
CG B:ASP402 3.1 55.0 1.0
CD2 B:HIS292 3.1 46.2 1.0
CG B:ASP293 3.2 45.7 1.0
CE1 B:HIS256 3.3 49.6 1.0
O B:HOH956 3.4 37.4 1.0
OD2 B:ASP402 3.4 62.5 1.0
CD2 B:HIS256 3.5 50.2 1.0
OD1 B:ASP293 3.6 44.9 1.0
O B:HOH955 3.6 53.9 1.0
MG B:MG902 3.7 44.6 1.0
CE1 B:HIS292 3.7 46.2 1.0
CD2 B:HIS252 3.9 43.7 1.0
NE2 B:HIS252 4.0 43.3 1.0
CG B:HIS292 4.4 44.3 1.0
O B:ASP402 4.4 44.8 1.0
CB B:ASP402 4.4 41.7 1.0
CB B:ASP293 4.5 38.8 1.0
O B:HOH959 4.5 29.0 1.0
ND1 B:HIS256 4.5 50.6 1.0
CG B:HIS256 4.6 48.7 1.0
ND1 B:HIS292 4.7 46.6 1.0
CA B:ASP402 4.8 40.1 1.0

Reference:

P.R.Verhoest, C.Proulx-Lafrance, M.Corman, L.Chenard, C.J.Helal, X.Hou, R.Kleiman, S.Liu, E.Marr, F.S.Menniti, C.J.Schmidt, M.Vanase-Frawley, A.W.Schmidt, R.D.Williams, F.R.Nelson, K.R.Fonseca, S.Liras. Identification of A Brain Penetrant PDE9A Inhibitor Utilizing Prospective Design and Chemical Enablement As A Rapid Lead Optimization Strategy. J.Med.Chem. V. 52 7946 2009.
ISSN: ISSN 0022-2623
PubMed: 19919087
DOI: 10.1021/JM9015334
Page generated: Sat Oct 26 07:29:53 2024

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