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Magnesium in PDB 5k1i: PDE4 Crystal Structure in Complex with Small Molecule Inhibitor

Enzymatic activity of PDE4 Crystal Structure in Complex with Small Molecule Inhibitor

All present enzymatic activity of PDE4 Crystal Structure in Complex with Small Molecule Inhibitor:
3.1.4.53;

Protein crystallography data

The structure of PDE4 Crystal Structure in Complex with Small Molecule Inhibitor, PDB code: 5k1i was solved by V.Segarra, B.Hernandez, N.Ferrer-Miralles, I.Korndoerfer, J.Aymami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.61
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 61.444, 78.347, 161.756, 91.01, 92.79, 90.08
R / Rfree (%) 19.1 / 25.8

Other elements in 5k1i:

The structure of PDE4 Crystal Structure in Complex with Small Molecule Inhibitor also contains other interesting chemical elements:

Zinc (Zn) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the PDE4 Crystal Structure in Complex with Small Molecule Inhibitor (pdb code 5k1i). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the PDE4 Crystal Structure in Complex with Small Molecule Inhibitor, PDB code: 5k1i:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5k1i

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Magnesium binding site 1 out of 8 in the PDE4 Crystal Structure in Complex with Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of PDE4 Crystal Structure in Complex with Small Molecule Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1003

b:42.5
occ:1.00
 OD1 A:ASP201 2.0 25.2 1.0
CG A:ASP201 3.0 25.4 1.0
OD2 A:ASP201 3.3 23.3 1.0
O A:HIS200 3.7 27.8 1.0
ZN A:ZN1002 3.7 37.1 1.0
CD2 A:HIS200 3.8 25.5 1.0
OG1 A:THR271 4.0 23.1 1.0
NE2 A:HIS233 4.2 28.7 1.0
OD2 A:ASP318 4.3 24.8 1.0
O A:THR271 4.4 24.5 1.0
CB A:ASP201 4.4 26.0 1.0
NE2 A:HIS200 4.5 26.2 1.0
OE2 A:GLU230 4.5 26.9 1.0
CD2 A:HIS233 4.5 27.8 1.0
O2 A:6PT1001 4.6 32.2 1.0
CB A:THR271 4.6 22.2 1.0
C A:HIS200 4.6 26.1 1.0
CD2 A:HIS204 4.8 26.2 1.0
CA A:ASP201 4.8 25.4 1.0
NE2 A:HIS160 4.9 26.8 1.0
CG A:HIS200 4.9 24.8 1.0
CD2 A:HIS160 4.9 26.4 1.0
OD1 A:ASP318 4.9 23.1 1.0
CG A:ASP318 5.0 23.6 1.0

Magnesium binding site 2 out of 8 in 5k1i

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Magnesium binding site 2 out of 8 in the PDE4 Crystal Structure in Complex with Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of PDE4 Crystal Structure in Complex with Small Molecule Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1003

b:37.2
occ:1.00
 OD1 B:ASP201 2.1 19.6 1.0
CG B:ASP201 3.3 19.3 1.0
NE2 B:HIS233 3.7 21.9 1.0
CD2 B:HIS233 3.8 21.2 1.0
O B:HIS200 3.8 20.6 1.0
OD2 B:ASP201 3.8 19.0 1.0
OG1 B:THR271 4.0 17.4 1.0
OE2 B:GLU230 4.1 23.6 1.0
CD2 B:HIS200 4.2 18.0 1.0
ZN B:ZN1002 4.3 29.0 1.0
CG B:GLU230 4.4 21.3 1.0
CB B:ASP201 4.5 19.0 1.0
CD B:GLU230 4.6 22.6 1.0
CD2 B:HIS204 4.6 15.8 1.0
O3 B:6PT1001 4.7 28.8 1.0
CA B:ASP201 4.7 18.8 1.0
C B:HIS200 4.7 18.6 1.0
OD2 B:ASP318 4.8 18.8 1.0
CE1 B:HIS233 4.8 21.8 1.0
NE2 B:HIS200 4.8 19.0 1.0
NE2 B:HIS204 4.9 15.8 1.0
CB B:THR271 4.9 17.6 1.0

Magnesium binding site 3 out of 8 in 5k1i

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Magnesium binding site 3 out of 8 in the PDE4 Crystal Structure in Complex with Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of PDE4 Crystal Structure in Complex with Small Molecule Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1003

b:38.5
occ:1.00
 OD1 C:ASP201 2.2 20.0 1.0
CG C:ASP201 3.1 18.9 1.0
OD2 C:ASP201 3.3 18.9 1.0
ZN C:ZN1002 3.7 32.9 1.0
O3 C:6PT1001 3.9 31.3 1.0
CD2 C:HIS200 4.2 20.1 1.0
O C:HIS200 4.2 20.1 1.0
OD2 C:ASP318 4.2 17.9 1.0
NE2 C:HIS233 4.4 23.6 1.0
OE2 C:GLU230 4.4 20.8 1.0
NE2 C:HIS160 4.5 18.9 1.0
CB C:ASP201 4.5 18.8 1.0
OG1 C:THR271 4.5 18.5 1.0
CD2 C:HIS204 4.5 18.4 1.0
NE2 C:HIS200 4.5 20.7 1.0
CD2 C:HIS233 4.6 21.9 1.0
NE2 C:HIS204 4.7 18.9 1.0
CD2 C:HIS160 4.7 18.3 1.0
C20 C:6PT1001 4.8 30.3 1.0
C18 C:6PT1001 4.8 29.1 1.0
O C:THR271 4.9 19.5 1.0
CB C:THR271 4.9 17.3 1.0
O C:HOH1102 4.9 10.7 1.0
CA C:ASP201 5.0 19.0 1.0
CG C:GLU230 5.0 19.0 1.0

Magnesium binding site 4 out of 8 in 5k1i

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Magnesium binding site 4 out of 8 in the PDE4 Crystal Structure in Complex with Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of PDE4 Crystal Structure in Complex with Small Molecule Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1003

b:34.2
occ:1.00
 OD1 D:ASP201 1.9 17.4 1.0
CG D:ASP201 3.0 17.8 1.0
OD2 D:ASP201 3.4 18.3 1.0
ZN D:ZN1002 3.8 33.8 1.0
O D:HIS200 4.1 19.3 1.0
NE2 D:HIS233 4.2 19.7 1.0
CD2 D:HIS200 4.2 17.8 1.0
OE2 D:GLU230 4.2 19.2 1.0
OG1 D:THR271 4.3 16.0 1.0
CB D:ASP201 4.4 18.4 1.0
CD2 D:HIS233 4.4 19.9 1.0
O2 D:6PT1001 4.5 31.1 1.0
CD2 D:HIS204 4.5 15.0 1.0
NE2 D:HIS200 4.6 18.9 1.0
OD2 D:ASP318 4.7 19.8 1.0
CA D:ASP201 4.7 17.8 1.0
CD2 D:HIS160 4.8 16.2 1.0
NE2 D:HIS160 4.8 16.8 1.0
NE2 D:HIS204 4.8 14.7 1.0
C D:HIS200 5.0 19.1 1.0
C18 D:6PT1001 5.0 29.9 1.0
C20 D:6PT1001 5.0 30.0 1.0

Magnesium binding site 5 out of 8 in 5k1i

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Magnesium binding site 5 out of 8 in the PDE4 Crystal Structure in Complex with Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of PDE4 Crystal Structure in Complex with Small Molecule Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1003

b:38.6
occ:1.00
 OD1 E:ASP201 2.0 19.6 1.0
CG E:ASP201 2.9 18.9 1.0
OD2 E:ASP201 3.1 18.3 1.0
ZN E:ZN1002 3.6 31.1 1.0
CD2 E:HIS200 4.2 18.9 1.0
OD2 E:ASP318 4.2 19.4 1.0
O2 E:6PT1001 4.2 31.1 1.0
CB E:ASP201 4.4 19.7 1.0
OG1 E:THR271 4.4 13.8 1.0
NE2 E:HIS160 4.5 18.0 1.0
OE2 E:GLU230 4.5 23.4 1.0
O E:HIS200 4.5 20.2 1.0
CD2 E:HIS160 4.5 17.6 1.0
NE2 E:HIS233 4.6 21.1 1.0
NE2 E:HIS200 4.7 18.5 1.0
CD2 E:HIS204 4.8 15.9 1.0
C20 E:6PT1001 4.8 30.1 1.0
O E:THR271 4.8 17.0 1.0
C18 E:6PT1001 4.8 29.4 1.0
CD2 E:HIS233 4.8 20.2 1.0
CA E:ASP201 4.9 19.1 1.0
CB E:THR271 4.9 14.4 1.0

Magnesium binding site 6 out of 8 in 5k1i

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Magnesium binding site 6 out of 8 in the PDE4 Crystal Structure in Complex with Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of PDE4 Crystal Structure in Complex with Small Molecule Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1003

b:37.2
occ:1.00
 OD1 F:ASP201 1.9 26.0 1.0
CG F:ASP201 2.9 26.1 1.0
OD2 F:ASP201 3.3 26.3 1.0
O F:HIS200 3.8 27.9 1.0
ZN F:ZN1002 3.8 37.0 1.0
NE2 F:HIS233 4.0 28.6 1.0
CD2 F:HIS200 4.0 28.1 1.0
OE2 F:GLU230 4.1 28.2 1.0
CB F:ASP201 4.2 26.9 1.0
O3 F:6PT1001 4.2 32.5 1.0
CD2 F:HIS233 4.3 27.3 1.0
CD2 F:HIS204 4.4 26.8 1.0
NE2 F:HIS200 4.5 29.4 1.0
OD2 F:ASP318 4.5 27.6 1.0
OG1 F:THR271 4.5 22.7 1.0
CA F:ASP201 4.6 26.8 1.0
NE2 F:HIS204 4.6 27.3 1.0
NE2 F:HIS160 4.6 28.6 1.0
CD2 F:HIS160 4.7 28.1 1.0
C F:HIS200 4.7 27.0 1.0
CD F:GLU230 4.9 27.7 1.0
CB F:THR271 5.0 23.3 1.0
C20 F:6PT1001 5.0 31.4 1.0

Magnesium binding site 7 out of 8 in 5k1i

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Magnesium binding site 7 out of 8 in the PDE4 Crystal Structure in Complex with Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of PDE4 Crystal Structure in Complex with Small Molecule Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg1003

b:35.9
occ:1.00
 OD1 G:ASP201 2.1 15.6 1.0
CG G:ASP201 3.2 16.4 1.0
OD2 G:ASP201 3.7 16.4 1.0
ZN G:ZN1002 3.8 26.7 1.0
O G:HIS200 3.9 17.5 1.0
OE2 G:GLU230 3.9 19.5 1.0
OG1 G:THR271 4.0 16.1 1.0
CD2 G:HIS200 4.0 17.4 1.0
OD2 G:ASP318 4.2 16.0 1.0
NE2 G:HIS233 4.2 17.9 1.0
CD2 G:HIS233 4.4 18.6 1.0
O3 G:6PT1001 4.4 30.6 1.0
CB G:ASP201 4.5 17.2 1.0
NE2 G:HIS200 4.5 18.6 1.0
CB G:THR271 4.6 16.4 1.0
CA G:ASP201 4.7 17.4 1.0
CD G:GLU230 4.7 18.1 1.0
CG G:GLU230 4.8 17.8 1.0
C G:HIS200 4.8 18.1 1.0
CD2 G:HIS204 4.8 15.5 1.0

Magnesium binding site 8 out of 8 in 5k1i

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Magnesium binding site 8 out of 8 in the PDE4 Crystal Structure in Complex with Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of PDE4 Crystal Structure in Complex with Small Molecule Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg1003

b:39.0
occ:1.00
 OD1 H:ASP201 2.4 19.5 1.0
CG H:ASP201 3.5 19.7 1.0
OE2 H:GLU230 3.8 22.7 1.0
OD2 H:ASP201 3.9 20.6 1.0
O H:HIS200 3.9 20.0 1.0
NE2 H:HIS233 4.0 21.6 1.0
ZN H:ZN1002 4.0 36.3 1.0
CD2 H:HIS200 4.1 21.0 1.0
OG1 H:THR271 4.1 16.4 1.0
CD2 H:HIS233 4.2 20.9 1.0
OD2 H:ASP318 4.4 21.5 1.0
O2 H:6PT1001 4.5 31.2 1.0
CG H:GLU230 4.6 19.8 1.0
CD H:GLU230 4.6 21.0 1.0
NE2 H:HIS200 4.6 22.0 1.0
CD2 H:HIS204 4.7 17.6 1.0
CB H:ASP201 4.7 19.5 1.0
CB H:THR271 4.8 16.0 1.0
NE2 H:HIS160 4.8 17.5 1.0
O H:THR271 4.8 19.3 1.0
C H:HIS200 4.9 19.8 1.0
CA H:ASP201 4.9 19.2 1.0
CD2 H:HIS160 4.9 17.2 1.0
NE2 H:HIS204 5.0 18.5 1.0

Reference:

J.Gracia, M.A.Buil, J.Castro, P.Eichhorn, M.Ferrer, A.Gavalda, B.Hernandez, V.Segarra, M.D.Lehner, I.Moreno, L.Pages, R.S.Roberts, J.Serrat, S.Sevilla, J.Taltavull, M.Andres, J.Cabedo, D.Vilella, E.Calama, C.Carcasona, M.Miralpeix. Biphenyl Pyridazinone Derivatives As Inhaled PDE4 Inhibitors: Structural Biology and Structure-Activity Relationships. J. Med. Chem. V. 59 10479 2016.
ISSN: ISSN 1520-4804
PubMed: 27933955
DOI: 10.1021/ACS.JMEDCHEM.6B00829
Page generated: Sun Sep 29 18:49:53 2024

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