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Fluorine in PDB 5wh6: Crystal Structure of PDE4D2 in Complex with Inhibitor (S_ZL-N-91)

Enzymatic activity of Crystal Structure of PDE4D2 in Complex with Inhibitor (S_ZL-N-91)

All present enzymatic activity of Crystal Structure of PDE4D2 in Complex with Inhibitor (S_ZL-N-91):
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of PDE4D2 in Complex with Inhibitor (S_ZL-N-91), PDB code: 5wh6 was solved by H.Ke, H.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 58.948, 80.197, 163.670, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 22.4

Other elements in 5wh6:

The structure of Crystal Structure of PDE4D2 in Complex with Inhibitor (S_ZL-N-91) also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms
Zinc (Zn) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of PDE4D2 in Complex with Inhibitor (S_ZL-N-91) (pdb code 5wh6). 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 PDE4D2 in Complex with Inhibitor (S_ZL-N-91), PDB code: 5wh6:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 5wh6

Go back to Fluorine Binding Sites List in 5wh6
Fluorine binding site 1 out of 4 in the Crystal Structure of PDE4D2 in Complex with Inhibitor (S_ZL-N-91)


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 PDE4D2 in Complex with Inhibitor (S_ZL-N-91) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:22.3
occ:1.00
 F1 A:AKJ601 0.0 22.3 1.0
C1 A:AKJ601 1.4 21.5 1.0
F2 A:AKJ601 2.2 21.5 1.0
O1 A:AKJ601 2.3 20.6 1.0
C2 A:AKJ601 2.9 21.2 1.0
C7 A:AKJ601 3.1 21.6 1.0
C A:TRP332 3.3 17.2 1.0
O A:TRP332 3.3 17.3 1.0
OD1 A:ASN321 3.4 17.7 1.0
N A:THR333 3.4 17.5 1.0
CB A:TRP332 3.5 16.7 1.0
CA A:THR333 3.6 18.1 1.0
OG1 A:THR333 3.8 19.0 1.0
CG2 A:ILE336 3.8 19.6 1.0
CA A:TRP332 4.0 16.8 1.0
CB A:ASN321 4.1 17.2 1.0
CG A:ASN321 4.1 17.2 1.0
C3 A:AKJ601 4.1 21.9 1.0
CE1 A:TYR159 4.1 15.9 1.0
CB A:ILE336 4.3 19.2 1.0
CB A:THR333 4.3 18.6 1.0
C6 A:AKJ601 4.3 22.3 1.0
CE1 A:TYR329 4.6 17.9 1.0
O2 A:AKJ601 4.6 21.8 1.0
NE2 A:GLN369 4.7 19.7 1.0
OE1 A:GLN369 4.7 19.4 1.0
O A:TYR329 4.7 18.0 1.0
CD1 A:TYR159 4.8 15.9 1.0
CD1 A:TYR329 4.8 17.6 1.0
C A:THR333 4.8 18.4 1.0
CG A:TRP332 4.8 17.0 1.0
OH A:TYR159 4.9 16.1 1.0
CZ A:TYR159 4.9 16.1 1.0

Fluorine binding site 2 out of 4 in 5wh6

Go back to Fluorine Binding Sites List in 5wh6
Fluorine binding site 2 out of 4 in the Crystal Structure of PDE4D2 in Complex with Inhibitor (S_ZL-N-91)


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 PDE4D2 in Complex with Inhibitor (S_ZL-N-91) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:21.5
occ:1.00
 F2 A:AKJ601 0.0 21.5 1.0
C1 A:AKJ601 1.4 21.5 1.0
F1 A:AKJ601 2.2 22.3 1.0
O1 A:AKJ601 2.3 20.6 1.0
C2 A:AKJ601 2.9 21.2 1.0
C7 A:AKJ601 3.0 21.6 1.0
CB A:ASN321 3.3 17.2 1.0
CE1 A:TYR329 3.5 17.9 1.0
OD1 A:ASN321 3.6 17.7 1.0
CG A:PRO322 3.6 17.9 1.0
OE1 A:GLN369 3.7 19.4 1.0
CD A:PRO322 3.7 17.9 1.0
CE2 A:PHE372 3.8 21.0 1.0
CG A:ASN321 3.9 17.2 1.0
CD1 A:TYR329 4.0 17.6 1.0
N A:PRO322 4.2 17.7 1.0
O A:HOH827 4.2 19.3 1.0
C3 A:AKJ601 4.2 21.9 1.0
CD2 A:PHE372 4.3 20.9 1.0
OG1 A:THR333 4.4 19.0 1.0
C6 A:AKJ601 4.4 22.3 1.0
CA A:ASN321 4.5 17.1 1.0
CD A:GLN369 4.5 19.8 1.0
NE2 A:GLN369 4.6 19.7 1.0
C A:ASN321 4.6 17.5 1.0
CZ A:TYR329 4.6 18.3 1.0
O2 A:AKJ601 4.8 21.8 1.0
CB A:PRO322 4.8 18.0 1.0
CZ A:PHE372 4.8 20.8 1.0
CB A:TRP332 4.8 16.7 1.0
OH A:TYR329 4.8 18.1 1.0
CA A:PRO322 4.9 18.1 1.0

Fluorine binding site 3 out of 4 in 5wh6

Go back to Fluorine Binding Sites List in 5wh6
Fluorine binding site 3 out of 4 in the Crystal Structure of PDE4D2 in Complex with Inhibitor (S_ZL-N-91)


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 PDE4D2 in Complex with Inhibitor (S_ZL-N-91) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:24.0
occ:1.00
 F1 B:AKJ601 0.0 24.0 1.0
C1 B:AKJ601 1.4 23.4 1.0
F2 B:AKJ601 2.3 23.5 1.0
O1 B:AKJ601 2.3 23.6 1.0
C2 B:AKJ601 2.9 24.6 1.0
C7 B:AKJ601 3.1 25.5 1.0
C B:TRP332 3.3 21.8 1.0
O B:TRP332 3.3 21.4 1.0
N B:THR333 3.4 22.0 1.0
OD1 B:ASN321 3.4 20.5 1.0
CB B:TRP332 3.5 22.4 1.0
CA B:THR333 3.6 22.4 1.0
OG1 B:THR333 3.8 22.4 1.0
CG2 B:ILE336 3.8 21.4 1.0
CA B:TRP332 4.0 22.2 1.0
CB B:ASN321 4.0 20.4 1.0
CG B:ASN321 4.1 20.5 1.0
C3 B:AKJ601 4.2 25.2 1.0
CE1 B:TYR159 4.2 17.7 1.0
CB B:ILE336 4.3 21.1 1.0
CB B:THR333 4.3 22.6 1.0
C6 B:AKJ601 4.4 26.6 1.0
CE1 B:TYR329 4.6 19.0 1.0
O2 B:AKJ601 4.6 24.4 1.0
O B:TYR329 4.6 20.7 1.0
OE1 B:GLN369 4.7 21.9 1.0
CD1 B:TYR329 4.7 18.9 1.0
NE2 B:GLN369 4.7 22.4 1.0
C B:THR333 4.8 22.4 1.0
CG B:TRP332 4.8 22.7 1.0
CD1 B:TYR159 4.8 18.2 1.0
CZ B:TYR159 5.0 18.2 1.0
OH B:TYR159 5.0 18.4 1.0
CD B:GLN369 5.0 22.2 1.0

Fluorine binding site 4 out of 4 in 5wh6

Go back to Fluorine Binding Sites List in 5wh6
Fluorine binding site 4 out of 4 in the Crystal Structure of PDE4D2 in Complex with Inhibitor (S_ZL-N-91)


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 PDE4D2 in Complex with Inhibitor (S_ZL-N-91) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:23.5
occ:1.00
 F2 B:AKJ601 0.0 23.5 1.0
C1 B:AKJ601 1.4 23.4 1.0
F1 B:AKJ601 2.3 24.0 1.0
O1 B:AKJ601 2.3 23.6 1.0
C2 B:AKJ601 2.9 24.6 1.0
C7 B:AKJ601 3.0 25.5 1.0
CB B:ASN321 3.2 20.4 1.0
CE1 B:TYR329 3.5 19.0 1.0
CG B:PRO322 3.6 20.4 1.0
OD1 B:ASN321 3.6 20.5 1.0
OE1 B:GLN369 3.7 21.9 1.0
CD B:PRO322 3.7 20.2 1.0
CE2 B:PHE372 3.8 22.3 1.0
CG B:ASN321 3.9 20.5 1.0
CD1 B:TYR329 4.0 18.9 1.0
O B:HOH783 4.2 20.4 1.0
C3 B:AKJ601 4.2 25.2 1.0
N B:PRO322 4.2 20.1 1.0
C6 B:AKJ601 4.3 26.6 1.0
CD2 B:PHE372 4.3 22.3 1.0
CA B:ASN321 4.4 20.7 1.0
OG1 B:THR333 4.4 22.4 1.0
CD B:GLN369 4.5 22.2 1.0
C B:ASN321 4.5 20.1 1.0
CZ B:TYR329 4.6 18.8 1.0
NE2 B:GLN369 4.6 22.4 1.0
O2 B:AKJ601 4.7 24.4 1.0
CZ B:PHE372 4.8 22.0 1.0
OH B:TYR329 4.8 19.3 1.0
CB B:TRP332 4.8 22.4 1.0
CB B:PRO322 4.8 20.4 1.0
CA B:PRO322 5.0 20.2 1.0
N B:ASN321 5.0 20.8 1.0

Reference:

X.Feng, H.Wang, M.Ye, X.T.Xu, Y.Xu, W.Yang, H.T.Zhang, G.Song, H.Ke. Identification of A PDE4-Specific Pocket For the Design of Selective Inhibitors. Biochemistry V. 57 4518 2018.
ISSN: ISSN 0006-2960
PubMed: 29975048
DOI: 10.1021/ACS.BIOCHEM.8B00336
Page generated: Tue Jul 15 09:00:04 2025

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