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Fluorine in PDB 7f2m: Crystal Structure of PDE4D Catalytic Domain Complexed with Compound 18D

Enzymatic activity of Crystal Structure of PDE4D Catalytic Domain Complexed with Compound 18D

All present enzymatic activity of Crystal Structure of PDE4D Catalytic Domain Complexed with Compound 18D:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of PDE4D Catalytic Domain Complexed with Compound 18D, PDB code: 7f2m was solved by Y.-Y.Huang, X.He, H.-B.Luo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.21 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.487, 80.157, 162.787, 90, 90, 90
R / Rfree (%) 19.8 / 24.7

Other elements in 7f2m:

The structure of Crystal Structure of PDE4D Catalytic Domain Complexed with Compound 18D also contains other interesting chemical elements:

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

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of PDE4D Catalytic Domain Complexed with Compound 18D (pdb code 7f2m). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of PDE4D Catalytic Domain Complexed with Compound 18D, PDB code: 7f2m:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 7f2m

Go back to Fluorine Binding Sites List in 7f2m
Fluorine binding site 1 out of 2 in the Crystal Structure of PDE4D Catalytic Domain Complexed with Compound 18D


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 PDE4D Catalytic Domain Complexed with Compound 18D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F603

b:35.3
occ:1.00
F38 A:1GF603 0.0 35.3 1.0
C35 A:1GF603 1.4 26.5 1.0
C34 A:1GF603 2.3 25.6 1.0
C36 A:1GF603 2.3 23.7 1.0
O A:GLY371 2.7 23.0 1.0
C A:GLY371 2.8 22.6 1.0
N A:PHE372 3.3 18.3 1.0
CA A:GLY371 3.4 19.3 1.0
CD2 A:TYR375 3.6 30.6 1.0
C33 A:1GF603 3.6 29.8 1.0
C37 A:1GF603 3.6 22.9 1.0
CA A:PHE372 3.6 20.6 1.0
CB A:TYR375 3.8 20.2 1.0
CG A:TYR375 4.0 29.9 1.0
C32 A:1GF603 4.1 25.4 1.0
CE2 A:TYR375 4.5 31.4 1.0
C A:PHE372 4.6 14.9 1.0
CB A:PHE372 4.7 16.6 1.0
N A:GLY371 4.7 19.2 1.0
N A:TYR375 4.8 18.5 1.0
O A:SER368 4.9 18.1 1.0
CA A:TYR375 4.9 20.3 1.0

Fluorine binding site 2 out of 2 in 7f2m

Go back to Fluorine Binding Sites List in 7f2m
Fluorine binding site 2 out of 2 in the Crystal Structure of PDE4D Catalytic Domain Complexed with Compound 18D


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 PDE4D Catalytic Domain Complexed with Compound 18D within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F603

b:45.7
occ:1.00
F38 B:1GF603 0.0 45.7 1.0
C35 B:1GF603 1.4 36.5 1.0
C34 B:1GF603 2.3 31.9 1.0
C36 B:1GF603 2.3 34.7 1.0
O B:GLY371 2.7 31.4 1.0
C B:GLY371 2.8 27.3 1.0
CA B:GLY371 3.3 24.7 1.0
N B:PHE372 3.4 25.7 1.0
CD2 B:TYR375 3.4 36.3 1.0
C33 B:1GF603 3.6 37.4 1.0
C37 B:1GF603 3.6 30.7 1.0
CA B:PHE372 3.8 26.0 1.0
CB B:TYR375 3.9 27.2 1.0
CG B:TYR375 3.9 38.9 1.0
C32 B:1GF603 4.1 34.1 1.0
CE2 B:TYR375 4.3 43.0 1.0
N B:GLY371 4.6 25.1 1.0
CB B:PHE372 4.8 22.4 1.0
N B:TYR375 4.8 28.4 1.0
C B:PHE372 4.9 27.7 1.0
CA B:TYR375 5.0 27.4 1.0

Reference:

Y.Y.Huang, J.Deng, Y.J.Tian, J.Liang, X.Xie, Y.Huang, J.Zhu, Z.Zhu, Q.Zhou, X.He, H.B.Luo. Mangostanin Derivatives As Novel and Orally Active Phosphodiesterase 4 Inhibitors For the Treatment of Idiopathic Pulmonary Fibrosis with Improved Safety. J.Med.Chem. V. 64 13736 2021.
ISSN: ISSN 0022-2623
PubMed: 34520193
DOI: 10.1021/ACS.JMEDCHEM.1C01085
Page generated: Fri Nov 5 13:12:20 2021

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