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Fluorine in PDB 3k3h: Crystal Structure of the PDE9A Catalytic Domain in Complex with (S)- BAY73-6691

Enzymatic activity of Crystal Structure of the PDE9A Catalytic Domain in Complex with (S)- BAY73-6691

All present enzymatic activity of Crystal Structure of the PDE9A Catalytic Domain in Complex with (S)- BAY73-6691:
3.1.4.35;

Protein crystallography data

The structure of Crystal Structure of the PDE9A Catalytic Domain in Complex with (S)- BAY73-6691, PDB code: 3k3h was solved by H.Wang, X.Luo, M.Ye, J.Hou, H.Robinson, H.Ke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.50
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 103.272, 103.272, 271.098, 90.00, 90.00, 90.00
R / Rfree (%) 22.3 / 24.5

Other elements in 3k3h:

The structure of Crystal Structure of the PDE9A Catalytic Domain in Complex with (S)- 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 the PDE9A Catalytic Domain in Complex with (S)- BAY73-6691 (pdb code 3k3h). 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 the PDE9A Catalytic Domain in Complex with (S)- BAY73-6691, PDB code: 3k3h:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3k3h

Go back to Fluorine Binding Sites List in 3k3h
Fluorine binding site 1 out of 6 in the Crystal Structure of the PDE9A Catalytic Domain in Complex with (S)- 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 the PDE9A Catalytic Domain in Complex with (S)- BAY73-6691 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F600

b:56.3
occ:1.00
 F5 A:BYE600 0.0 56.3 1.0
C21 A:BYE600 1.4 53.4 1.0
F6 A:BYE600 2.2 54.5 1.0
F7 A:BYE600 2.2 57.2 1.0
C19 A:BYE600 2.4 51.6 1.0
C18 A:BYE600 2.8 47.0 1.0
C20 A:BYE600 2.9 47.1 1.0
CB A:ALA452 2.9 51.4 1.0
CA A:ALA452 3.9 52.5 1.0
C A:ALA452 4.2 51.9 1.0
C14 A:BYE600 4.3 43.6 1.0
O A:ALA452 4.4 50.9 1.0
CB A:PHE441 4.4 62.9 1.0
CG2 A:VAL447 4.4 67.9 1.0
O A:PHE441 4.5 62.6 1.0
OE1 A:GLN453 4.6 48.0 1.0
CD1 A:PHE441 4.7 61.4 1.0
N A:GLN453 4.8 50.5 1.0
N15 A:BYE600 5.0 39.1 1.0
CG A:PHE441 5.0 62.2 1.0

Fluorine binding site 2 out of 6 in 3k3h

Go back to Fluorine Binding Sites List in 3k3h
Fluorine binding site 2 out of 6 in the Crystal Structure of the PDE9A Catalytic Domain in Complex with (S)- 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 the PDE9A Catalytic Domain in Complex with (S)- BAY73-6691 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F600

b:54.5
occ:1.00
 F6 A:BYE600 0.0 54.5 1.0
C21 A:BYE600 1.4 53.4 1.0
F7 A:BYE600 2.2 57.2 1.0
F5 A:BYE600 2.2 56.3 1.0
C19 A:BYE600 2.4 51.6 1.0
C18 A:BYE600 2.9 47.0 1.0
CD1 A:PHE441 3.0 61.4 1.0
CG A:PHE441 3.5 62.2 1.0
CB A:PHE441 3.6 62.9 1.0
C20 A:BYE600 3.7 47.1 1.0
CE2 A:TYR424 3.7 46.1 1.0
CE1 A:PHE441 3.8 60.4 1.0
C14 A:BYE600 4.2 43.6 1.0
O A:PHE441 4.2 62.6 1.0
CD2 A:TYR424 4.4 47.0 1.0
N13 A:BYE600 4.5 43.4 1.0
CD2 A:PHE441 4.7 61.1 1.0
OH A:TYR424 4.7 44.7 1.0
CZ A:TYR424 4.7 45.4 1.0
C A:PHE441 4.7 62.5 1.0
CA A:PHE441 4.8 63.2 1.0
CZ A:PHE441 4.8 60.5 1.0

Fluorine binding site 3 out of 6 in 3k3h

Go back to Fluorine Binding Sites List in 3k3h
Fluorine binding site 3 out of 6 in the Crystal Structure of the PDE9A Catalytic Domain in Complex with (S)- 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 the PDE9A Catalytic Domain in Complex with (S)- BAY73-6691 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F600

b:57.2
occ:1.00
 F7 A:BYE600 0.0 57.2 1.0
C21 A:BYE600 1.4 53.4 1.0
F6 A:BYE600 2.2 54.5 1.0
F5 A:BYE600 2.2 56.3 1.0
C19 A:BYE600 2.4 51.6 1.0
C20 A:BYE600 2.8 47.1 1.0
O A:PHE441 3.3 62.6 1.0
CE2 A:TYR424 3.4 46.1 1.0
CD2 A:TYR424 3.5 47.0 1.0
CD2 A:LEU421 3.7 44.3 1.0
C18 A:BYE600 3.7 47.0 1.0
CD1 A:PHE441 3.8 61.4 1.0
CG2 A:VAL447 4.2 67.9 1.0
C A:PHE441 4.3 62.5 1.0
CB A:PHE441 4.4 62.9 1.0
CB A:ALA452 4.5 51.4 1.0
CG A:PHE441 4.6 62.2 1.0
CZ A:TYR424 4.7 45.4 1.0
CE1 A:PHE441 4.7 60.4 1.0
CG A:LEU421 4.7 45.0 1.0
CG A:TYR424 4.8 47.0 1.0
C14 A:BYE600 4.8 43.6 1.0
CA A:PHE441 4.8 63.2 1.0

Fluorine binding site 4 out of 6 in 3k3h

Go back to Fluorine Binding Sites List in 3k3h
Fluorine binding site 4 out of 6 in the Crystal Structure of the PDE9A Catalytic Domain in Complex with (S)- 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 the PDE9A Catalytic Domain in Complex with (S)- BAY73-6691 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F600

b:57.0
occ:1.00
 F5 B:BYE600 0.0 57.0 1.0
C21 B:BYE600 1.4 53.3 1.0
F6 B:BYE600 2.2 55.9 1.0
F7 B:BYE600 2.2 54.2 1.0
C19 B:BYE600 2.4 52.2 1.0
C20 B:BYE600 2.8 48.7 1.0
C18 B:BYE600 2.9 47.7 1.0
CB B:ALA452 3.0 50.1 1.0
CA B:ALA452 4.0 50.7 1.0
C14 B:BYE600 4.3 46.7 1.0
C B:ALA452 4.3 49.4 1.0
OE1 B:GLN453 4.4 45.2 1.0
CG2 B:VAL447 4.5 67.9 1.0
CB B:PHE441 4.6 58.3 1.0
O B:ALA452 4.6 48.5 1.0
N B:GLN453 4.9 47.6 1.0
N15 B:BYE600 4.9 46.2 1.0
O B:PHE441 5.0 58.2 1.0

Fluorine binding site 5 out of 6 in 3k3h

Go back to Fluorine Binding Sites List in 3k3h
Fluorine binding site 5 out of 6 in the Crystal Structure of the PDE9A Catalytic Domain in Complex with (S)- 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 the PDE9A Catalytic Domain in Complex with (S)- BAY73-6691 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F600

b:55.9
occ:1.00
 F6 B:BYE600 0.0 55.9 1.0
C21 B:BYE600 1.4 53.3 1.0
F5 B:BYE600 2.2 57.0 1.0
F7 B:BYE600 2.2 54.2 1.0
C19 B:BYE600 2.4 52.2 1.0
C18 B:BYE600 2.8 47.7 1.0
CD1 B:PHE441 3.5 61.0 1.0
C20 B:BYE600 3.7 48.7 1.0
CG B:PHE441 3.8 60.4 1.0
CB B:PHE441 3.8 58.3 1.0
CE2 B:TYR424 4.0 44.9 1.0
C14 B:BYE600 4.1 46.7 1.0
CE1 B:PHE441 4.2 61.1 1.0
N13 B:BYE600 4.5 46.1 1.0
CD2 B:TYR424 4.7 44.1 1.0
CD2 B:PHE441 4.7 59.7 1.0
O B:PHE441 4.7 58.2 1.0
OH B:TYR424 4.9 44.6 1.0
CZ B:TYR424 4.9 44.5 1.0

Fluorine binding site 6 out of 6 in 3k3h

Go back to Fluorine Binding Sites List in 3k3h
Fluorine binding site 6 out of 6 in the Crystal Structure of the PDE9A Catalytic Domain in Complex with (S)- 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 the PDE9A Catalytic Domain in Complex with (S)- BAY73-6691 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F600

b:54.2
occ:1.00
 F7 B:BYE600 0.0 54.2 1.0
C21 B:BYE600 1.4 53.3 1.0
F6 B:BYE600 2.2 55.9 1.0
F5 B:BYE600 2.2 57.0 1.0
C19 B:BYE600 2.4 52.2 1.0
C20 B:BYE600 2.9 48.7 1.0
CE2 B:TYR424 3.4 44.9 1.0
CD2 B:TYR424 3.6 44.1 1.0
O B:PHE441 3.6 58.2 1.0
C18 B:BYE600 3.7 47.7 1.0
CD2 B:LEU421 3.8 44.9 1.0
CD1 B:PHE441 4.0 61.0 1.0
CB B:PHE441 4.2 58.3 1.0
CG2 B:VAL447 4.5 67.9 1.0
CG B:PHE441 4.6 60.4 1.0
C B:PHE441 4.6 58.3 1.0
CB B:ALA452 4.7 50.1 1.0
CZ B:TYR424 4.7 44.5 1.0
C14 B:BYE600 4.8 46.7 1.0
CG B:LEU421 4.8 47.5 1.0
CG B:TYR424 4.9 44.8 1.0
CA B:PHE441 5.0 57.5 1.0
CE1 B:PHE441 5.0 61.1 1.0

Reference:

H.Wang, X.Luo, M.Ye, J.Hou, H.Robinson, H.Ke. Insight Into Binding of Phosphodiesterase-9A Selective Inhibitors By Crystal Structures and Mutagenesis J.Med.Chem. V. 53 1726 2010.
ISSN: ISSN 0022-2623
PubMed: 20121115
DOI: 10.1021/JM901519F
Page generated: Mon Jul 14 17:13:05 2025

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