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Zinc in PDB 4kp6: Crystal Structure of Human Phosphodiesterase 4B (PDE4B) in Complex with A [1,3,5]Triazine Derivative

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 4B (PDE4B) in Complex with A [1,3,5]Triazine Derivative

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 4B (PDE4B) in Complex with A [1,3,5]Triazine Derivative:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 4B (PDE4B) in Complex with A [1,3,5]Triazine Derivative, PDB code: 4kp6 was solved by R.Gewald, C.Grunwald, U.Egerland, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 57.26 / 1.50
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 53.332, 53.332, 229.048, 90.00, 90.00, 90.00
R / Rfree (%) 16.8 / 19.8

Other elements in 4kp6:

The structure of Crystal Structure of Human Phosphodiesterase 4B (PDE4B) in Complex with A [1,3,5]Triazine Derivative also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Phosphodiesterase 4B (PDE4B) in Complex with A [1,3,5]Triazine Derivative (pdb code 4kp6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of Human Phosphodiesterase 4B (PDE4B) in Complex with A [1,3,5]Triazine Derivative, PDB code: 4kp6:

Zinc binding site 1 out of 1 in 4kp6

Go back to Zinc Binding Sites List in 4kp6
Zinc binding site 1 out of 1 in the Crystal Structure of Human Phosphodiesterase 4B (PDE4B) in Complex with A [1,3,5]Triazine Derivative


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 Human Phosphodiesterase 4B (PDE4B) in Complex with A [1,3,5]Triazine Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:12.5
occ:1.00
 OD2 A:ASP275 2.1 10.6 1.0
OD1 A:ASP392 2.1 10.4 1.0
NE2 A:HIS238 2.1 10.7 1.0
NE2 A:HIS274 2.1 8.7 1.0
O A:HOH712 2.2 10.4 1.0
O A:HOH711 2.2 9.9 1.0
CG A:ASP392 3.1 9.9 1.0
CD2 A:HIS274 3.1 9.7 1.0
CD2 A:HIS238 3.1 11.8 1.0
CG A:ASP275 3.1 8.8 1.0
CE1 A:HIS238 3.1 8.7 1.0
CE1 A:HIS274 3.2 9.2 1.0
OD2 A:ASP392 3.4 12.8 1.0
OD1 A:ASP275 3.6 10.9 1.0
MG A:MG502 3.8 9.9 1.0
O A:HOH726 4.0 15.7 1.0
O A:HOH646 4.0 10.8 1.0
CG A:HIS274 4.2 10.1 1.0
ND1 A:HIS274 4.2 9.3 1.0
ND1 A:HIS238 4.2 11.5 1.0
CD2 A:HIS234 4.2 16.5 1.0
CG A:HIS238 4.3 9.7 1.0
CB A:ASP275 4.3 8.9 1.0
CB A:ASP392 4.4 9.6 1.0
NE2 A:HIS234 4.4 14.5 1.0
CG2 A:VAL242 4.7 10.1 1.0
O A:HOH612 4.7 10.5 1.0
CA A:ASP392 4.9 8.8 1.0

Reference:

R.Gewald, C.Grunwald, U.Egerland. Discovery of Triazines As Potent, Selective and Orally Active PDE4 Inhibitors. Bioorg.Med.Chem.Lett. V. 23 4308 2013.
ISSN: ISSN 0960-894X
PubMed: 23806553
DOI: 10.1016/J.BMCL.2013.05.099
Page generated: Sun Oct 27 01:20:59 2024

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