Fluorine in PDB 2fm0: Crystal Structure of PDE4D in Complex with L-869298

All present enzymatic activity of Crystal Structure of PDE4D in Complex with L-869298:
3.1.4.17;

The structure of Crystal Structure of PDE4D in Complex with L-869298, PDB code: 2fm0 was solved by Q.Huai, Y.Sun, H.Wang, D.Macdonald, R.Aspiotis, H.Robinson, Z.Huang, H.Ke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	99.511, 112.176, 160.174, 90.00, 90.00, 90.00
R / Rfree (%)	22.3 / 24.5

The structure of Crystal Structure of PDE4D in Complex with L-869298 also contains other interesting chemical elements:

Magnesium	(Mg)	4 atoms
Zinc	(Zn)	4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 32;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of PDE4D in Complex with L-869298 (pdb code 2fm0). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 32 binding sites of Fluorine where determined in the Crystal Structure of PDE4D in Complex with L-869298, PDB code: 2fm0:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 32 in the Crystal Structure of PDE4D in Complex with L-869298


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 in Complex with L-869298 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:25.8 occ:1.00 F1 A:M98601 0.0 25.8 1.0 C1 A:M98601 1.3 25.7 1.0 F2 A:M98601 2.2 26.6 1.0 O1 A:M98601 2.2 27.2 1.0 C7 A:M98601 2.9 26.9 1.0 C2 A:M98601 2.9 27.5 1.0 C A:TRP332 3.1 24.0 1.0 N A:THR333 3.2 24.9 1.0 O A:TRP332 3.2 24.6 1.0 CB A:TRP332 3.3 23.1 1.0 OD1 A:ASN321 3.3 22.7 1.0 CA A:THR333 3.5 24.6 1.0 CA A:TRP332 3.8 24.2 1.0 CG2 A:ILE336 3.8 24.7 1.0 OG1 A:THR333 3.8 24.9 1.0 CB A:ASN321 3.9 21.5 1.0 CG A:ASN321 4.0 22.4 1.0 CE1 A:TYR159 4.1 20.5 1.0 C3 A:M98601 4.2 28.1 1.0 C6 A:M98601 4.3 27.8 1.0 CB A:ILE336 4.3 24.4 1.0 CB A:THR333 4.3 24.8 1.0 O A:TYR329 4.5 26.3 1.0 CG A:TRP332 4.6 23.5 1.0 CE1 A:TYR329 4.6 24.8 1.0 C A:THR333 4.7 25.0 1.0 CD1 A:TYR329 4.7 24.7 1.0 CD1 A:TYR159 4.7 20.7 1.0 O2 A:M98601 4.8 29.2 1.0 OE1 A:GLN369 4.8 23.4 1.0 NE2 A:GLN369 4.9 24.1 1.0 CZ A:TYR159 4.9 21.3 1.0 OH A:TYR159 4.9 20.6 1.0 N A:TRP332 4.9 23.7 1.0

Fluorine binding site 2 out of 32 in the Crystal Structure of PDE4D in Complex with L-869298


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 in Complex with L-869298 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:26.6 occ:1.00 F2 A:M98601 0.0 26.6 1.0 C1 A:M98601 1.4 25.7 1.0 F1 A:M98601 2.2 25.8 1.0 O1 A:M98601 2.3 27.2 1.0 C2 A:M98601 2.8 27.5 1.0 C7 A:M98601 2.8 26.9 1.0 CB A:ASN321 3.2 21.5 1.0 CE1 A:TYR329 3.5 24.8 1.0 CG A:PRO322 3.6 23.9 1.0 CE2 A:PHE372 3.7 26.1 1.0 OE1 A:GLN369 3.7 23.4 1.0 CD A:PRO322 3.7 23.0 1.0 OD1 A:ASN321 3.7 22.7 1.0 C3 A:M98601 4.0 28.1 1.0 CG A:ASN321 4.0 22.4 1.0 CD1 A:TYR329 4.0 24.7 1.0 C6 A:M98601 4.1 27.8 1.0 N A:PRO322 4.2 23.6 1.0 CD2 A:PHE372 4.2 25.1 1.0 O A:HOH620 4.2 21.6 1.0 OG1 A:THR333 4.3 24.9 1.0 CA A:ASN321 4.4 22.8 1.0 CD A:GLN369 4.5 25.0 1.0 C A:ASN321 4.5 23.1 1.0 O2 A:M98601 4.5 29.2 1.0 CZ A:TYR329 4.5 25.3 1.0 NE2 A:GLN369 4.6 24.1 1.0 CZ A:PHE372 4.7 24.8 1.0 CB A:TRP332 4.7 23.1 1.0 OH A:TYR329 4.8 25.1 1.0 CB A:PRO322 4.8 23.8 1.0 CA A:PRO322 4.9 23.9 1.0 C4 A:M98601 4.9 27.6 1.0 N A:THR333 5.0 24.9 1.0 C5 A:M98601 5.0 28.2 1.0

Fluorine binding site 3 out of 32 in the Crystal Structure of PDE4D in Complex with L-869298


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 PDE4D in Complex with L-869298 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:39.0 occ:1.00 F5 A:M98601 0.0 39.0 1.0 C16 A:M98601 1.3 39.2 1.0 F7 A:M98601 2.2 39.2 1.0 F6 A:M98601 2.2 39.9 1.0 C15 A:M98601 2.4 42.0 1.0 F9 A:M98601 2.7 39.1 1.0 O3 A:M98601 2.8 38.2 1.0 C17 A:M98601 2.9 39.3 1.0 O A:HOH615 3.2 30.7 1.0 F10 A:M98601 3.4 39.6 1.0 C14 A:M98601 3.7 34.5 1.0 CE A:MET357 3.7 32.2 1.0 F8 A:M98601 4.2 39.2 1.0 C11 A:M98601 4.4 32.5 1.0 S1 A:M98601 4.9 30.1 1.0

Fluorine binding site 4 out of 32 in the Crystal Structure of PDE4D in Complex with L-869298


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 PDE4D in Complex with L-869298 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:39.9 occ:1.00 F6 A:M98601 0.0 39.9 1.0 C16 A:M98601 1.3 39.2 1.0 F5 A:M98601 2.2 39.0 1.0 F7 A:M98601 2.2 39.2 1.0 C15 A:M98601 2.4 42.0 1.0 O3 A:M98601 2.8 38.2 1.0 C14 A:M98601 2.8 34.5 1.0 C13 A:M98601 3.1 29.8 1.0 CE A:MET357 3.3 32.2 1.0 C11 A:M98601 3.5 32.5 1.0 S1 A:M98601 3.7 30.1 1.0 C17 A:M98601 3.7 39.3 1.0 F10 A:M98601 4.1 39.6 1.0 C12 A:M98601 4.1 30.3 1.0 F9 A:M98601 4.2 39.1 1.0 O A:HOH615 4.3 30.7 1.0 SD A:MET357 4.3 33.2 1.0 N1 A:M98601 4.4 30.5 1.0 C8 A:M98601 4.5 29.4 1.0 CD1 A:ILE376 4.5 31.5 1.0 C10 A:M98601 4.6 29.9 1.0 CD1 A:PHE372 4.7 25.3 1.0 F8 A:M98601 4.7 39.2 1.0

Fluorine binding site 5 out of 32 in the Crystal Structure of PDE4D in Complex with L-869298


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 PDE4D in Complex with L-869298 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:39.2 occ:1.00 F7 A:M98601 0.0 39.2 1.0 C16 A:M98601 1.4 39.2 1.0 F5 A:M98601 2.2 39.0 1.0 F6 A:M98601 2.2 39.9 1.0 C15 A:M98601 2.4 42.0 1.0 F10 A:M98601 2.5 39.6 1.0 C11 A:M98601 2.8 32.5 1.0 C14 A:M98601 2.9 34.5 1.0 C17 A:M98601 2.9 39.3 1.0 CD1 A:ILE376 3.0 31.5 1.0 F9 A:M98601 3.4 39.1 1.0 O3 A:M98601 3.6 38.2 1.0 F8 A:M98601 4.1 39.2 1.0 N1 A:M98601 4.2 30.5 1.0 S1 A:M98601 4.4 30.1 1.0 CG1 A:ILE376 4.5 30.8 1.0 CE A:MET273 4.6 25.6 1.0 C13 A:M98601 4.9 29.8 1.0 C10 A:M98601 4.9 29.9 1.0

Fluorine binding site 6 out of 32 in the Crystal Structure of PDE4D in Complex with L-869298


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 PDE4D in Complex with L-869298 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:39.2 occ:1.00 F8 A:M98601 0.0 39.2 1.0 C17 A:M98601 1.3 39.3 1.0 F10 A:M98601 2.2 39.6 1.0 F9 A:M98601 2.2 39.1 1.0 C15 A:M98601 2.4 42.0 1.0 C14 A:M98601 2.8 34.5 1.0 O3 A:M98601 2.9 38.2 1.0 C11 A:M98601 3.4 32.5 1.0 CG A:MET273 3.6 24.8 1.0 CB A:MET273 3.7 25.4 1.0 C16 A:M98601 3.7 39.2 1.0 S1 A:M98601 3.8 30.1 1.0 O A:HOH613 4.0 46.8 1.0 F7 A:M98601 4.1 39.2 1.0 F5 A:M98601 4.2 39.0 1.0 O4 A:M98601 4.2 33.5 1.0 N1 A:M98601 4.4 30.5 1.0 O A:HOH615 4.4 30.7 1.0 N2 A:M98601 4.5 30.4 1.0 C22 A:M98601 4.6 30.3 1.0 C10 A:M98601 4.6 29.9 1.0 F6 A:M98601 4.7 39.9 1.0 O A:HOH608 4.8 31.4 1.0

Fluorine binding site 7 out of 32 in the Crystal Structure of PDE4D in Complex with L-869298


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of PDE4D in Complex with L-869298 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:39.1 occ:1.00 F9 A:M98601 0.0 39.1 1.0 C17 A:M98601 1.3 39.3 1.0 F10 A:M98601 2.2 39.6 1.0 F8 A:M98601 2.2 39.2 1.0 C15 A:M98601 2.4 42.0 1.0 F5 A:M98601 2.7 39.0 1.0 O3 A:M98601 2.8 38.2 1.0 C16 A:M98601 3.0 39.2 1.0 O A:HOH615 3.2 30.7 1.0 F7 A:M98601 3.4 39.2 1.0 C14 A:M98601 3.7 34.5 1.0 F6 A:M98601 4.2 39.9 1.0 C11 A:M98601 4.4 32.5 1.0 S1 A:M98601 5.0 30.1 1.0

Fluorine binding site 8 out of 32 in the Crystal Structure of PDE4D in Complex with L-869298


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of PDE4D in Complex with L-869298 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:39.6 occ:1.00 F10 A:M98601 0.0 39.6 1.0 C17 A:M98601 1.3 39.3 1.0 F8 A:M98601 2.2 39.2 1.0 F9 A:M98601 2.2 39.1 1.0 C15 A:M98601 2.4 42.0 1.0 F7 A:M98601 2.5 39.2 1.0 C11 A:M98601 2.8 32.5 1.0 C16 A:M98601 2.9 39.2 1.0 C14 A:M98601 2.9 34.5 1.0 F5 A:M98601 3.4 39.0 1.0 CB A:MET273 3.5 25.4 1.0 CG A:MET273 3.6 24.8 1.0 O3 A:M98601 3.6 38.2 1.0 CE A:MET273 3.7 25.6 1.0 F6 A:M98601 4.1 39.9 1.0 N1 A:M98601 4.2 30.5 1.0 S1 A:M98601 4.5 30.1 1.0 SD A:MET273 4.5 25.1 1.0 CD1 A:ILE376 4.6 31.5 1.0 C10 A:M98601 5.0 29.9 1.0 CA A:MET273 5.0 26.4 1.0

Fluorine binding site 9 out of 32 in the Crystal Structure of PDE4D in Complex with L-869298


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of PDE4D in Complex with L-869298 within 5.0Å range: probe atom residue distance (Å) B Occ B:F602 b:30.4 occ:1.00 F1 B:M98602 0.0 30.4 1.0 C1 B:M98602 1.3 29.4 1.0 F2 B:M98602 2.2 29.9 1.0 O1 B:M98602 2.3 30.1 1.0 C7 B:M98602 2.9 29.7 1.0 C2 B:M98602 2.9 29.9 1.0 OD1 B:ASN321 3.1 30.3 1.0 C B:TRP332 3.2 31.1 1.0 N B:THR333 3.3 31.2 1.0 O B:TRP332 3.3 31.1 1.0 CB B:TRP332 3.3 30.6 1.0 CA B:THR333 3.5 30.9 1.0 CB B:ASN321 3.8 30.2 1.0 CA B:TRP332 3.8 31.3 1.0 CG B:ASN321 3.9 30.4 1.0 OG1 B:THR333 3.9 31.5 1.0 CG2 B:ILE336 3.9 28.8 1.0 CE1 B:TYR159 4.1 26.0 1.0 C3 B:M98602 4.2 30.1 1.0 C6 B:M98602 4.2 30.1 1.0 CB B:THR333 4.4 31.5 1.0 CB B:ILE336 4.4 28.5 1.0 CG B:TRP332 4.5 30.4 1.0 O B:TYR329 4.6 33.3 1.0 CE1 B:TYR329 4.6 28.3 1.0 CD1 B:TYR329 4.7 29.9 1.0 O2 B:M98602 4.8 30.6 1.0 CD1 B:TYR159 4.8 25.8 1.0 C B:THR333 4.8 31.2 1.0 OE1 B:GLN369 4.8 30.1 1.0 CZ B:TYR159 4.9 26.9 1.0 OH B:TYR159 4.9 26.5 1.0 NE2 B:GLN369 4.9 30.9 1.0 N B:TRP332 5.0 31.4 1.0

Fluorine binding site 10 out of 32 in the Crystal Structure of PDE4D in Complex with L-869298


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of PDE4D in Complex with L-869298 within 5.0Å range: probe atom residue distance (Å) B Occ B:F602 b:29.9 occ:1.00 F2 B:M98602 0.0 29.9 1.0 C1 B:M98602 1.3 29.4 1.0 F1 B:M98602 2.2 30.4 1.0 O1 B:M98602 2.3 30.1 1.0 C2 B:M98602 2.8 29.9 1.0 C7 B:M98602 2.8 29.7 1.0 CB B:ASN321 3.2 30.2 1.0 CE1 B:TYR329 3.5 28.3 1.0 CG B:PRO322 3.6 30.6 1.0 CE2 B:PHE372 3.6 30.9 1.0 OE1 B:GLN369 3.6 30.1 1.0 OD1 B:ASN321 3.7 30.3 1.0 CD B:PRO322 3.7 30.1 1.0 CG B:ASN321 3.9 30.4 1.0 C3 B:M98602 3.9 30.1 1.0 CD1 B:TYR329 4.0 29.9 1.0 C6 B:M98602 4.1 30.1 1.0 CD2 B:PHE372 4.2 30.9 1.0 N B:PRO322 4.2 30.2 1.0 OG1 B:THR333 4.3 31.5 1.0 CA B:ASN321 4.4 30.3 1.0 CD B:GLN369 4.4 31.4 1.0 O B:HOH641 4.5 27.0 1.0 O2 B:M98602 4.5 30.6 1.0 C B:ASN321 4.5 30.3 1.0 NE2 B:GLN369 4.5 30.9 1.0 CZ B:TYR329 4.6 28.3 1.0 CZ B:PHE372 4.7 31.0 1.0 OH B:TYR329 4.8 26.0 1.0 CB B:TRP332 4.8 30.6 1.0 CB B:PRO322 4.9 30.0 1.0 C4 B:M98602 4.9 30.4 1.0 CA B:PRO322 5.0 31.2 1.0 C5 B:M98602 5.0 30.5 1.0 N B:THR333 5.0 31.2 1.0

Q.Huai, Y.Sun, H.Wang, D.Macdonald, R.Aspiotis, H.Robinson, Z.Huang, H.Ke. Enantiomer Discrimination Illustrated By the High Resolution Crystal Structures of Type 4 Phosphodiesterase J.Med.Chem. V. 49 1867 2006.
ISSN: ISSN 0022-2623
PubMed: 16539372
DOI: 10.1021/JM051273D