Fluorine in PDB 7vtv: Crystal Structure of PDE8A Catalytic Domain in Complex with 15

Enzymatic activity of Crystal Structure of PDE8A Catalytic Domain in Complex with 15

All present enzymatic activity of Crystal Structure of PDE8A Catalytic Domain in Complex with 15:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of PDE8A Catalytic Domain in Complex with 15, PDB code: 7vtv was solved by X.-N.Wu, Q.Zhou, Y.-D.Huang, Z.Li, Y.Wu, H.-B.Luo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.17 / 2.80
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 75.986, 131.724, 101.456, 90, 90, 90
R / Rfree (%) 28.2 / 32.4

Other elements in 7vtv:

The structure of Crystal Structure of PDE8A Catalytic Domain in Complex with 15 also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Zinc (Zn) 1 atom
Chlorine (Cl) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of PDE8A Catalytic Domain in Complex with 15 (pdb code 7vtv). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of PDE8A Catalytic Domain in Complex with 15, PDB code: 7vtv:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 7vtv

Go back to Fluorine Binding Sites List in 7vtv
Fluorine binding site 1 out of 4 in the Crystal Structure of PDE8A Catalytic Domain in Complex with 15


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 PDE8A Catalytic Domain in Complex with 15 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F903

b:33.3
occ:1.00
FAU A:7ZZ903 0.0 33.3 1.0
CAT A:7ZZ903 1.4 32.7 1.0
FAV A:7ZZ903 2.3 33.0 1.0
CAS A:7ZZ903 2.4 32.2 1.0
O A:THR668 2.6 26.4 1.0
O A:HOH1037 2.7 28.3 1.0
O A:GLU669 3.1 27.9 1.0
C A:GLU669 3.4 28.3 1.0
C A:THR668 3.4 26.2 1.0
CA A:MET670 3.6 29.5 1.0
OAR A:7ZZ903 3.6 31.1 1.0
N A:MET670 3.7 28.9 1.0
N A:GLU669 4.2 27.1 1.0
CA A:THR668 4.2 25.6 1.0
NZ A:LYS723 4.3 17.8 1.0
CA A:GLU669 4.3 27.8 1.0
CB A:MET670 4.5 30.0 1.0
CAP A:7ZZ903 4.6 30.0 1.0
C A:MET670 4.6 29.4 1.0
O A:MET670 4.7 29.7 1.0
ND1 A:HIS673 4.8 26.8 1.0
CG A:MET670 4.8 30.4 1.0
O A:ALA667 4.8 23.9 1.0
OD2 A:ASP726 4.9 17.4 1.0

Fluorine binding site 2 out of 4 in 7vtv

Go back to Fluorine Binding Sites List in 7vtv
Fluorine binding site 2 out of 4 in the Crystal Structure of PDE8A Catalytic Domain in Complex with 15


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 PDE8A Catalytic Domain in Complex with 15 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F903

b:33.0
occ:1.00
FAV A:7ZZ903 0.0 33.0 1.0
CAT A:7ZZ903 1.4 32.7 1.0
FAU A:7ZZ903 2.3 33.3 1.0
CAS A:7ZZ903 2.4 32.2 1.0
OAR A:7ZZ903 2.6 31.1 1.0
ND1 A:HIS673 3.2 26.8 1.0
CB A:HIS673 3.5 26.4 1.0
CA A:MET670 3.5 29.5 1.0
O A:MET670 3.7 29.7 1.0
CG A:HIS673 3.7 26.6 1.0
CAP A:7ZZ903 3.8 30.0 1.0
CG A:MET670 3.9 30.4 1.0
O A:GLU669 4.1 27.9 1.0
C A:MET670 4.1 29.4 1.0
CD2 A:PHE785 4.2 27.0 1.0
CAO A:7ZZ903 4.2 29.9 1.0
CB A:MET670 4.2 30.0 1.0
NZ A:LYS723 4.2 17.8 1.0
CE2 A:PHE785 4.2 27.2 1.0
CE1 A:HIS673 4.3 26.9 1.0
CA A:HIS673 4.3 26.4 1.0
N A:MET670 4.4 28.9 1.0
O A:HOH1037 4.4 28.3 1.0
C A:GLU669 4.5 28.3 1.0
N A:HIS673 4.8 27.0 1.0
SD A:MET670 4.8 31.1 1.0
O A:THR668 4.8 26.4 1.0
CAQ A:7ZZ903 4.9 29.4 1.0
CD2 A:HIS673 5.0 26.8 1.0

Fluorine binding site 3 out of 4 in 7vtv

Go back to Fluorine Binding Sites List in 7vtv
Fluorine binding site 3 out of 4 in the Crystal Structure of PDE8A Catalytic Domain in Complex with 15


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 PDE8A Catalytic Domain in Complex with 15 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F903

b:29.7
occ:1.00
FAZ A:7ZZ903 0.0 29.7 1.0
CAY A:7ZZ903 1.3 29.5 1.0
FBA A:7ZZ903 2.1 29.3 1.0
OAW A:7ZZ903 2.2 29.8 1.0
CAN A:7ZZ903 2.7 29.5 1.0
CD1 A:PHE781 3.1 23.4 1.0
CAM A:7ZZ903 3.3 29.3 1.0
CE1 A:PHE785 3.4 26.9 1.0
CE1 A:PHE781 3.4 23.2 1.0
CAO A:7ZZ903 3.5 29.9 1.0
CL2 A:7ZZ903 3.5 27.3 1.0
N3 A:7ZZ903 3.9 27.6 1.0
CZ A:PHE785 3.9 27.1 1.0
C2 A:7ZZ903 4.0 27.4 1.0
CD1 A:PHE785 4.0 26.7 1.0
CG A:PHE781 4.3 23.4 1.0
CAL A:7ZZ903 4.3 29.0 1.0
CAP A:7ZZ903 4.5 30.0 1.0
CZ A:PHE781 4.7 23.2 1.0
CZ A:PHE767 4.8 35.9 1.0
CB A:PHE781 4.8 23.5 1.0
CAQ A:7ZZ903 4.8 29.4 1.0
C4 A:7ZZ903 4.9 27.8 1.0
CE2 A:PHE785 4.9 27.2 1.0

Fluorine binding site 4 out of 4 in 7vtv

Go back to Fluorine Binding Sites List in 7vtv
Fluorine binding site 4 out of 4 in the Crystal Structure of PDE8A Catalytic Domain in Complex with 15


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 PDE8A Catalytic Domain in Complex with 15 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F903

b:29.3
occ:1.00
FBA A:7ZZ903 0.0 29.3 1.0
CAY A:7ZZ903 1.3 29.5 1.0
FAZ A:7ZZ903 2.1 29.7 1.0
OAW A:7ZZ903 2.3 29.8 1.0
CAN A:7ZZ903 3.1 29.5 1.0
CAM A:7ZZ903 3.2 29.3 1.0
CL2 A:7ZZ903 3.4 27.3 1.0
CE1 A:PHE767 3.6 35.9 1.0
CE2 A:TYR748 3.7 30.9 1.0
OH A:TYR748 3.8 31.3 1.0
CZ A:PHE767 3.9 35.9 1.0
N3 A:7ZZ903 3.9 27.6 1.0
CZ A:TYR748 3.9 31.1 1.0
C2 A:7ZZ903 4.2 27.4 1.0
CAO A:7ZZ903 4.3 29.9 1.0
CAL A:7ZZ903 4.5 29.0 1.0
CD2 A:TYR748 4.5 30.9 1.0
CD1 A:PHE767 4.7 35.9 1.0
CE1 A:TYR748 4.9 31.2 1.0
CD1 A:PHE781 4.9 23.4 1.0

Reference:

X.-N.Wu, Q.Zhou, Y.-D.Huang, Z.Li, Y.Wu, H.-B.Luo. Structure-Based Discovery of Orally Efficient PDE8 Inhibitors For the Treatment of Vascular Dementia To Be Published.
Page generated: Wed Apr 5 01:39:30 2023

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy