Atomistry » Fluorine » PDB 3jx3-3kql » 3k3h
Atomistry »
  Fluorine »
    PDB 3jx3-3kql »
      3k3h »

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: Wed Jul 31 19:46:41 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy