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Fluorine in PDB 3k3e: Crystal Structure of the PDE9A Catalytic Domain in Complex with (R)- BAY73-6691

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

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

Protein crystallography data

The structure of Crystal Structure of the PDE9A Catalytic Domain in Complex with (R)- BAY73-6691, PDB code: 3k3e 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 / 2.70
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 103.190, 103.190, 270.849, 90.00, 90.00, 90.00
R / Rfree (%) 23 / 25.8

Other elements in 3k3e:

The structure of Crystal Structure of the PDE9A Catalytic Domain in Complex with (R)- 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 (R)- BAY73-6691 (pdb code 3k3e). 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 (R)- BAY73-6691, PDB code: 3k3e:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3k3e

Go back to Fluorine Binding Sites List in 3k3e
Fluorine binding site 1 out of 6 in the Crystal Structure of the PDE9A Catalytic Domain in Complex with (R)- 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 (R)- BAY73-6691 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F600

b:49.7
occ:1.00
F5 A:PDB600 0.0 49.7 1.0
C21 A:PDB600 1.4 51.7 1.0
F6 A:PDB600 2.2 51.9 1.0
F7 A:PDB600 2.2 50.8 1.0
C19 A:PDB600 2.4 51.7 1.0
C18 A:PDB600 2.7 49.1 1.0
C14 A:PDB600 2.8 48.9 1.0
N15 A:PDB600 2.8 47.7 1.0
OE1 A:GLN453 3.0 49.8 1.0
CD2 A:LEU420 3.4 46.5 1.0
CD A:GLN453 3.5 51.4 1.0
CG1 A:VAL417 3.6 43.4 1.0
N13 A:PDB600 3.6 48.7 1.0
C16 A:PDB600 3.7 47.5 1.0
C20 A:PDB600 3.7 49.8 1.0
NE2 A:GLN453 3.8 49.6 1.0
O17 A:PDB600 4.3 49.1 1.0
C11 A:PDB600 4.3 47.5 1.0
C12 A:PDB600 4.4 48.0 1.0
CB A:VAL417 4.4 46.5 1.0
CA A:VAL417 4.5 47.1 1.0
CG A:GLN453 4.5 50.9 1.0
O A:VAL417 4.5 50.7 1.0
CG A:LEU420 4.5 47.5 1.0
CG2 A:VAL417 4.6 45.8 1.0
CB A:LEU420 4.7 48.9 1.0

Fluorine binding site 2 out of 6 in 3k3e

Go back to Fluorine Binding Sites List in 3k3e
Fluorine binding site 2 out of 6 in the Crystal Structure of the PDE9A Catalytic Domain in Complex with (R)- 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 (R)- BAY73-6691 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F600

b:51.9
occ:1.00
F6 A:PDB600 0.0 51.9 1.0
C21 A:PDB600 1.4 51.7 1.0
F5 A:PDB600 2.2 49.7 1.0
F7 A:PDB600 2.2 50.8 1.0
C19 A:PDB600 2.4 51.7 1.0
C20 A:PDB600 2.7 49.8 1.0
C18 A:PDB600 3.1 49.1 1.0
CB A:ALA452 3.3 50.2 1.0
OE1 A:GLN453 3.4 49.8 1.0
C14 A:PDB600 4.0 48.9 1.0
CG1 A:VAL417 4.1 43.4 1.0
CD A:GLN453 4.1 51.4 1.0
CG A:LEU421 4.3 50.2 1.0
N15 A:PDB600 4.4 47.7 1.0
CD1 A:LEU421 4.4 48.3 1.0
CD2 A:LEU421 4.5 48.4 1.0
CG A:GLN453 4.6 50.9 1.0
CA A:ALA452 4.6 54.3 1.0
N A:GLN453 4.6 52.1 1.0
C A:ALA452 4.8 54.2 1.0
O A:LYS449 4.9 63.1 1.0
CD2 A:LEU420 4.9 46.5 1.0
NE2 A:GLN453 5.0 49.6 1.0
N13 A:PDB600 5.0 48.7 1.0

Fluorine binding site 3 out of 6 in 3k3e

Go back to Fluorine Binding Sites List in 3k3e
Fluorine binding site 3 out of 6 in the Crystal Structure of the PDE9A Catalytic Domain in Complex with (R)- 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 (R)- BAY73-6691 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F600

b:50.8
occ:1.00
F7 A:PDB600 0.0 50.8 1.0
C21 A:PDB600 1.4 51.7 1.0
F5 A:PDB600 2.2 49.7 1.0
F6 A:PDB600 2.2 51.9 1.0
C19 A:PDB600 2.4 51.7 1.0
C20 A:PDB600 3.0 49.8 1.0
CD2 A:LEU420 3.1 46.5 1.0
CG A:LEU421 3.4 50.2 1.0
CG A:LEU420 3.6 47.5 1.0
C18 A:PDB600 3.7 49.1 1.0
CD2 A:LEU421 3.7 48.4 1.0
CB A:LEU420 4.0 48.9 1.0
O A:VAL417 4.0 50.7 1.0
N A:LEU421 4.1 51.2 1.0
C14 A:PDB600 4.2 48.9 1.0
CD2 A:TYR424 4.2 50.3 1.0
CD1 A:LEU421 4.2 48.3 1.0
CE2 A:TYR424 4.2 49.9 1.0
CG1 A:VAL417 4.3 43.4 1.0
CB A:LEU421 4.4 49.1 1.0
CA A:LEU421 4.4 51.2 1.0
N13 A:PDB600 4.6 48.7 1.0
C A:LEU420 4.6 50.6 1.0
N15 A:PDB600 4.7 47.7 1.0
OE1 A:GLN453 4.9 49.8 1.0
C A:VAL417 5.0 49.6 1.0
CA A:LEU420 5.0 50.2 1.0

Fluorine binding site 4 out of 6 in 3k3e

Go back to Fluorine Binding Sites List in 3k3e
Fluorine binding site 4 out of 6 in the Crystal Structure of the PDE9A Catalytic Domain in Complex with (R)- 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 (R)- BAY73-6691 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F600

b:42.2
occ:1.00
F5 B:PDB600 0.0 42.2 1.0
C21 B:PDB600 1.4 44.1 1.0
F7 B:PDB600 2.2 45.5 1.0
F6 B:PDB600 2.2 47.3 1.0
C19 B:PDB600 2.4 42.6 1.0
C14 B:PDB600 2.8 43.1 1.0
N15 B:PDB600 2.8 41.8 1.0
C18 B:PDB600 2.9 42.6 1.0
OE1 B:GLN453 3.3 47.7 1.0
CD2 B:LEU420 3.4 49.5 1.0
N13 B:PDB600 3.5 44.7 1.0
C16 B:PDB600 3.6 43.0 1.0
C20 B:PDB600 3.7 40.5 1.0
CD B:GLN453 3.9 48.4 1.0
C11 B:PDB600 4.2 44.0 1.0
O17 B:PDB600 4.2 44.4 1.0
C12 B:PDB600 4.2 43.0 1.0
CG1 B:VAL417 4.2 47.5 1.0
NE2 B:GLN453 4.3 46.7 1.0
CG B:LEU420 4.4 51.3 1.0
CB B:LEU420 4.5 53.0 1.0
CG2 B:VAL417 4.5 45.1 1.0
CA B:VAL417 4.7 49.6 1.0
CB B:VAL417 4.7 48.7 1.0
O B:VAL417 4.7 52.5 1.0
CG B:GLN453 4.7 47.4 1.0

Fluorine binding site 5 out of 6 in 3k3e

Go back to Fluorine Binding Sites List in 3k3e
Fluorine binding site 5 out of 6 in the Crystal Structure of the PDE9A Catalytic Domain in Complex with (R)- 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 (R)- BAY73-6691 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F600

b:47.3
occ:1.00
F6 B:PDB600 0.0 47.3 1.0
C21 B:PDB600 1.4 44.1 1.0
F5 B:PDB600 2.2 42.2 1.0
F7 B:PDB600 2.2 45.5 1.0
C19 B:PDB600 2.4 42.6 1.0
C20 B:PDB600 2.8 40.5 1.0
C18 B:PDB600 2.8 42.6 1.0
OE1 B:GLN453 3.1 47.7 1.0
CB B:ALA452 3.2 49.0 1.0
C14 B:PDB600 3.7 43.1 1.0
N15 B:PDB600 3.9 41.8 1.0
CD B:GLN453 3.9 48.4 1.0
CG B:GLN453 4.2 47.4 1.0
N B:GLN453 4.3 47.3 1.0
CA B:ALA452 4.4 49.2 1.0
C B:ALA452 4.4 49.3 1.0
CG1 B:VAL417 4.6 47.5 1.0
N13 B:PDB600 4.8 44.7 1.0
NE2 B:GLN453 4.9 46.7 1.0
CA B:GLN453 4.9 46.9 1.0
O B:ALA452 5.0 49.9 1.0

Fluorine binding site 6 out of 6 in 3k3e

Go back to Fluorine Binding Sites List in 3k3e
Fluorine binding site 6 out of 6 in the Crystal Structure of the PDE9A Catalytic Domain in Complex with (R)- 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 (R)- BAY73-6691 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F600

b:45.5
occ:1.00
F7 B:PDB600 0.0 45.5 1.0
C21 B:PDB600 1.4 44.1 1.0
F5 B:PDB600 2.2 42.2 1.0
F6 B:PDB600 2.2 47.3 1.0
C19 B:PDB600 2.4 42.6 1.0
C20 B:PDB600 2.8 40.5 1.0
CG B:LEU421 3.6 51.6 1.0
CD2 B:LEU421 3.6 50.9 1.0
C18 B:PDB600 3.7 42.6 1.0
CD2 B:LEU420 4.0 49.5 1.0
CE2 B:TYR424 4.3 43.2 1.0
CD1 B:LEU421 4.3 49.8 1.0
C14 B:PDB600 4.3 43.1 1.0
CG B:LEU420 4.3 51.3 1.0
CD2 B:TYR424 4.4 46.7 1.0
O B:VAL417 4.4 52.5 1.0
CB B:LEU420 4.5 53.0 1.0
CG1 B:VAL417 4.5 47.5 1.0
N B:LEU421 4.7 55.3 1.0
N15 B:PDB600 4.8 41.8 1.0
CB B:LEU421 4.8 52.4 1.0
N13 B:PDB600 4.9 44.7 1.0
CB B:ALA452 4.9 49.0 1.0
CA B:LEU421 4.9 55.1 1.0
OE1 B:GLN453 4.9 47.7 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: Sun Dec 13 11:49:05 2020

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