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Fluorine in PDB 3qi3: Crystal Structure of PDE9A(Q453E) in Complex with Inhibitor BAY73-6691

Enzymatic activity of Crystal Structure of PDE9A(Q453E) in Complex with Inhibitor BAY73-6691

All present enzymatic activity of Crystal Structure of PDE9A(Q453E) in Complex with Inhibitor BAY73-6691:
3.1.4.35;

Protein crystallography data

The structure of Crystal Structure of PDE9A(Q453E) in Complex with Inhibitor BAY73-6691, PDB code: 3qi3 was solved by J.Hou, J.Xu, M.Liu, R.Zhao, H.Lou, H.Ke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.30
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 103.127, 103.127, 270.441, 90.00, 90.00, 90.00
R / Rfree (%) 22.2 / 24.2

Other elements in 3qi3:

The structure of Crystal Structure of PDE9A(Q453E) in Complex with Inhibitor BAY73-6691 also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Zinc (Zn) 2 atoms
Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of PDE9A(Q453E) in Complex with Inhibitor BAY73-6691 (pdb code 3qi3). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of PDE9A(Q453E) in Complex with Inhibitor BAY73-6691, PDB code: 3qi3:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3qi3

Go back to Fluorine Binding Sites List in 3qi3
Fluorine binding site 1 out of 6 in the Crystal Structure of PDE9A(Q453E) in Complex with Inhibitor BAY73-6691


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of PDE9A(Q453E) in Complex with Inhibitor BAY73-6691 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F600

b:70.8
occ:1.00
 F5 A:PDB600 0.0 70.8 1.0
C21 A:PDB600 1.4 67.2 1.0
F6 A:PDB600 2.2 66.8 1.0
F7 A:PDB600 2.2 66.5 1.0
C19 A:PDB600 2.4 65.3 1.0
C18 A:PDB600 2.8 61.2 1.0
CB A:ALA452 3.1 51.0 1.0
C A:ALA452 3.4 52.0 1.0
O A:ALA452 3.5 51.9 1.0
OE1 A:GLU453 3.5 62.0 1.0
C20 A:PDB600 3.7 68.6 1.0
N A:GLU453 3.7 51.7 1.0
CA A:ALA452 3.9 51.5 1.0
C14 A:PDB600 4.2 56.5 1.0
CA A:GLU453 4.2 51.8 1.0
CD A:GLU453 4.5 60.1 1.0
CG A:GLU453 4.6 58.5 1.0
CB A:PHE456 4.7 42.2 1.0
N15 A:PDB600 4.7 54.4 1.0
O A:LYS449 5.0 58.7 1.0
CB A:GLU453 5.0 53.8 1.0

Fluorine binding site 2 out of 6 in 3qi3

Go back to Fluorine Binding Sites List in 3qi3
Fluorine binding site 2 out of 6 in the Crystal Structure of PDE9A(Q453E) in Complex with Inhibitor BAY73-6691


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of PDE9A(Q453E) in Complex with Inhibitor BAY73-6691 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F600

b:66.8
occ:1.00
 F6 A:PDB600 0.0 66.8 1.0
C21 A:PDB600 1.4 67.2 1.0
F7 A:PDB600 2.2 66.5 1.0
F5 A:PDB600 2.2 70.8 1.0
C19 A:PDB600 2.4 65.3 1.0
C20 A:PDB600 2.8 68.6 1.0
C18 A:PDB600 2.9 61.2 1.0
CD1 A:PHE441 3.8 62.8 1.0
CB A:PHE441 4.1 64.4 1.0
CG A:PHE441 4.2 63.5 1.0
CB A:ALA452 4.3 51.0 1.0
C14 A:PDB600 4.3 56.5 1.0
CE2 A:TYR424 4.3 46.6 1.0
O A:PHE441 4.5 66.8 1.0
CE1 A:PHE441 4.6 62.4 1.0
N13 A:PDB600 4.8 53.3 1.0
O A:ALA452 4.8 51.9 1.0
CD2 A:TYR424 4.9 45.6 1.0

Fluorine binding site 3 out of 6 in 3qi3

Go back to Fluorine Binding Sites List in 3qi3
Fluorine binding site 3 out of 6 in the Crystal Structure of PDE9A(Q453E) in Complex with Inhibitor BAY73-6691


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of PDE9A(Q453E) in Complex with Inhibitor BAY73-6691 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F600

b:66.5
occ:1.00
 F7 A:PDB600 0.0 66.5 1.0
C21 A:PDB600 1.4 67.2 1.0
F6 A:PDB600 2.2 66.8 1.0
F5 A:PDB600 2.2 70.8 1.0
C19 A:PDB600 2.4 65.3 1.0
C20 A:PDB600 2.9 68.6 1.0
CD2 A:LEU421 3.5 49.4 1.0
C18 A:PDB600 3.7 61.2 1.0
O A:PHE441 3.9 66.8 1.0
CE2 A:TYR424 4.0 46.6 1.0
CD2 A:TYR424 4.0 45.6 1.0
CB A:ALA452 4.1 51.0 1.0
CG2 A:VAL447 4.2 78.7 1.0
CG A:LEU421 4.6 49.0 1.0
CD1 A:PHE441 4.6 62.8 1.0
C14 A:PDB600 4.8 56.5 1.0

Fluorine binding site 4 out of 6 in 3qi3

Go back to Fluorine Binding Sites List in 3qi3
Fluorine binding site 4 out of 6 in the Crystal Structure of PDE9A(Q453E) in Complex with Inhibitor BAY73-6691


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of PDE9A(Q453E) in Complex with Inhibitor BAY73-6691 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F600

b:81.2
occ:1.00
 F5 B:PDB600 0.0 81.2 1.0
C21 B:PDB600 1.4 80.2 1.0
F6 B:PDB600 2.2 81.7 1.0
F7 B:PDB600 2.2 81.2 1.0
C19 B:PDB600 2.4 77.3 1.0
OE1 B:GLU453 2.8 66.5 1.0
C18 B:PDB600 2.9 71.5 1.0
CD B:GLU453 3.6 64.6 1.0
C20 B:PDB600 3.7 78.5 1.0
CG B:GLU453 3.7 62.4 1.0
N B:GLU453 4.0 54.9 1.0
CB B:ALA452 4.0 55.9 1.0
CG1 B:VAL417 4.0 52.5 1.0
CA B:GLU453 4.2 55.2 1.0
C14 B:PDB600 4.2 67.4 1.0
C B:ALA452 4.3 55.1 1.0
CD2 B:LEU421 4.5 48.2 1.0
CB B:GLU453 4.5 57.1 1.0
O B:LYS449 4.6 60.1 1.0
N15 B:PDB600 4.7 65.5 1.0
O B:ALA452 4.8 54.4 1.0
CA B:ALA452 4.8 55.6 1.0
OE2 B:GLU453 4.8 66.1 1.0

Fluorine binding site 5 out of 6 in 3qi3

Go back to Fluorine Binding Sites List in 3qi3
Fluorine binding site 5 out of 6 in the Crystal Structure of PDE9A(Q453E) in Complex with Inhibitor BAY73-6691


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of PDE9A(Q453E) in Complex with Inhibitor BAY73-6691 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F600

b:81.7
occ:1.00
 F6 B:PDB600 0.0 81.7 1.0
C21 B:PDB600 1.4 80.2 1.0
F5 B:PDB600 2.2 81.2 1.0
F7 B:PDB600 2.2 81.2 1.0
C19 B:PDB600 2.3 77.3 1.0
C18 B:PDB600 2.7 71.5 1.0
CB B:ALA452 2.8 55.9 1.0
C20 B:PDB600 2.9 78.5 1.0
C B:ALA452 3.2 55.1 1.0
O B:ALA452 3.3 54.4 1.0
CA B:ALA452 3.5 55.6 1.0
N B:GLU453 3.5 54.9 1.0
OE1 B:GLU453 4.0 66.5 1.0
CA B:GLU453 4.1 55.2 1.0
C14 B:PDB600 4.2 67.4 1.0
CB B:PHE456 4.5 41.9 1.0
N13 B:PDB600 4.7 66.4 1.0
N B:ALA452 4.8 56.7 1.0
CD B:GLU453 4.9 64.6 1.0
CG B:GLU453 4.9 62.4 1.0

Fluorine binding site 6 out of 6 in 3qi3

Go back to Fluorine Binding Sites List in 3qi3
Fluorine binding site 6 out of 6 in the Crystal Structure of PDE9A(Q453E) in Complex with Inhibitor BAY73-6691


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of PDE9A(Q453E) in Complex with Inhibitor BAY73-6691 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F600

b:81.2
occ:1.00
 F7 B:PDB600 0.0 81.2 1.0
C21 B:PDB600 1.4 80.2 1.0
F6 B:PDB600 2.2 81.7 1.0
F5 B:PDB600 2.2 81.2 1.0
C19 B:PDB600 2.4 77.3 1.0
C20 B:PDB600 2.8 78.5 1.0
CB B:ALA452 3.3 55.9 1.0
CD2 B:LEU421 3.4 48.2 1.0
C18 B:PDB600 3.7 71.5 1.0
CG2 B:VAL447 4.3 62.8 1.0
CG B:LEU421 4.5 48.6 1.0
CA B:ALA452 4.7 55.6 1.0
O B:PHE441 4.7 52.5 1.0
C B:ALA452 4.8 55.1 1.0
C14 B:PDB600 4.8 67.4 1.0
N B:GLU453 5.0 54.9 1.0
OE1 B:GLU453 5.0 66.5 1.0
CD1 B:LEU421 5.0 50.0 1.0

Reference:

J.Hou, J.Xu, M.Liu, R.Zhao, H.B.Luo, H.Ke. Structural Asymmetry of Phosphodiesterase-9, Potential Protonation of A Glutamic Acid, and Role of the Invariant Glutamine. Plos One V. 6 18092 2011.
ISSN: ESSN 1932-6203
PubMed: 21483814
DOI: 10.1371/JOURNAL.PONE.0018092
Page generated: Sun Dec 13 11:53:52 2020

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