Fluorine in PDB 3f8s: Crystal Structure of Dipeptidyl Peptidase IV in Complex with Inhibitor

All present enzymatic activity of Crystal Structure of Dipeptidyl Peptidase IV in Complex with Inhibitor:
3.4.14.5;

The structure of Crystal Structure of Dipeptidyl Peptidase IV in Complex with Inhibitor, PDB code: 3f8s was solved by M.J.Ammirati, S.Liu, D.W.Piotrowski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.43
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.429, 67.141, 421.529, 90.00, 90.00, 90.00
R / Rfree (%)	24.3 / 29.5

The binding sites of Fluorine atom in the Crystal Structure of Dipeptidyl Peptidase IV in Complex with Inhibitor (pdb code 3f8s). 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 Dipeptidyl Peptidase IV in Complex with Inhibitor, PDB code: 3f8s:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Crystal Structure of Dipeptidyl Peptidase IV in Complex with Inhibitor


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 Dipeptidyl Peptidase IV in Complex with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F900 b:81.2 occ:1.00 F26 A:PF2900 0.0 81.2 1.0 C11 A:PF2900 1.3 78.6 1.0 F25 A:PF2900 2.2 79.8 1.0 C10 A:PF2900 2.2 79.1 1.0 C12 A:PF2900 2.4 76.8 1.0 N A:TYR631 2.9 80.2 1.0 CA A:TYR631 3.2 79.8 1.0 CB A:TYR631 3.3 80.3 1.0 OG A:SER630 3.4 78.9 1.0 N8 A:PF2900 3.4 77.4 1.0 C9 A:PF2900 3.4 79.1 1.0 C A:SER630 3.6 80.3 1.0 CD2 A:TYR631 3.6 79.4 1.0 CG A:TYR631 3.9 79.5 1.0 CG2 A:VAL656 4.0 77.9 1.0 CB A:SER630 4.1 79.8 1.0 O A:SER630 4.2 80.5 1.0 CA A:SER630 4.3 80.1 1.0 OH A:TYR547 4.4 79.7 1.0 C6 A:PF2900 4.6 76.0 1.0 C A:TYR631 4.7 79.8 1.0 CH2 A:TRP659 4.8 79.2 1.0 OH A:TYR666 4.8 78.9 1.0 CE2 A:TYR631 4.8 80.7 1.0 CB A:VAL656 5.0 78.1 1.0

Fluorine binding site 2 out of 4 in the Crystal Structure of Dipeptidyl Peptidase IV in Complex with Inhibitor


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 Dipeptidyl Peptidase IV in Complex with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F900 b:79.8 occ:1.00 F25 A:PF2900 0.0 79.8 1.0 C11 A:PF2900 1.3 78.6 1.0 C10 A:PF2900 2.2 79.1 1.0 F26 A:PF2900 2.2 81.2 1.0 C12 A:PF2900 2.4 76.8 1.0 C9 A:PF2900 2.6 79.1 1.0 N8 A:PF2900 2.9 77.4 1.0 CE2 A:TYR662 3.5 80.1 1.0 CG2 A:VAL656 3.6 77.9 1.0 CD2 A:TYR662 3.7 79.8 1.0 CZ3 A:TRP659 3.7 78.5 1.0 CE1 A:TYR666 3.8 78.3 1.0 CH2 A:TRP659 3.9 79.2 1.0 CZ A:TYR662 3.9 80.4 1.0 CG A:TYR662 4.2 79.1 1.0 CZ A:TYR666 4.2 79.2 1.0 C6 A:PF2900 4.2 76.0 1.0 CD1 A:TYR666 4.3 78.1 1.0 CD2 A:TYR631 4.3 79.4 1.0 CE1 A:TYR662 4.4 79.6 1.0 OH A:TYR666 4.5 78.9 1.0 CD1 A:TYR662 4.5 80.0 1.0 OH A:TYR662 4.5 80.9 1.0 CB A:VAL656 4.8 78.1 1.0 CG2 A:VAL711 4.9 74.8 1.0 CE2 A:TYR666 4.9 79.1 1.0 CE3 A:TRP659 4.9 78.6 1.0 OG A:SER630 5.0 78.9 1.0 CG A:TYR666 5.0 79.1 1.0

Fluorine binding site 3 out of 4 in the Crystal Structure of Dipeptidyl Peptidase IV in Complex with Inhibitor


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 Dipeptidyl Peptidase IV in Complex with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:F900 b:79.0 occ:1.00 F26 B:PF2900 0.0 79.0 1.0 C11 B:PF2900 1.3 78.8 1.0 F25 B:PF2900 2.2 78.4 1.0 C10 B:PF2900 2.3 78.7 1.0 C12 B:PF2900 2.4 78.4 1.0 N B:TYR631 3.0 80.2 1.0 CB B:TYR631 3.2 80.2 1.0 OG B:SER630 3.3 79.2 1.0 CA B:TYR631 3.3 79.8 1.0 N8 B:PF2900 3.4 77.6 1.0 C9 B:PF2900 3.5 78.4 1.0 CD2 B:TYR631 3.7 79.4 1.0 OH B:TYR547 3.8 79.4 1.0 C B:SER630 3.9 80.3 1.0 CG B:TYR631 3.9 79.4 1.0 CB B:SER630 4.0 79.7 1.0 OH B:TYR666 4.4 78.7 1.0 CA B:SER630 4.5 80.0 1.0 CZ B:TYR547 4.5 80.4 1.0 C6 B:PF2900 4.5 76.1 1.0 O B:SER630 4.7 80.7 1.0 CZ B:TYR666 4.7 79.2 1.0 CG2 B:VAL656 4.7 77.9 1.0 CE1 B:TYR547 4.8 81.4 1.0 C B:TYR631 4.8 79.8 1.0 CE2 B:TYR631 4.9 80.9 1.0

Fluorine binding site 4 out of 4 in the Crystal Structure of Dipeptidyl Peptidase IV in Complex with Inhibitor


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 Dipeptidyl Peptidase IV in Complex with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:F900 b:78.4 occ:1.00 F25 B:PF2900 0.0 78.4 1.0 C11 B:PF2900 1.3 78.8 1.0 F26 B:PF2900 2.2 79.0 1.0 C10 B:PF2900 2.2 78.7 1.0 C12 B:PF2900 2.3 78.4 1.0 C9 B:PF2900 3.0 78.4 1.0 N8 B:PF2900 3.2 77.6 1.0 CG2 B:VAL656 3.3 77.9 1.0 CE2 B:TYR662 3.8 80.0 1.0 CD2 B:TYR662 4.0 79.6 1.0 CZ3 B:TRP659 4.1 78.5 1.0 CZ B:TYR662 4.1 80.5 1.0 CH2 B:TRP659 4.1 79.1 1.0 CE1 B:TYR666 4.3 77.9 1.0 CG B:TYR662 4.4 79.3 1.0 CE1 B:TYR662 4.4 80.2 1.0 CD2 B:TYR631 4.4 79.4 1.0 OG B:SER630 4.5 79.2 1.0 CB B:VAL656 4.5 78.0 1.0 CG2 B:VAL711 4.5 74.7 1.0 CD1 B:TYR662 4.5 80.6 1.0 C6 B:PF2900 4.6 76.1 1.0 N B:TYR631 4.6 80.2 1.0 CZ B:TYR666 4.6 79.2 1.0 OH B:TYR662 4.6 81.0 1.0 OH B:TYR666 4.7 78.7 1.0 CA B:TYR631 4.8 79.8 1.0 CD1 B:TYR666 4.8 77.6 1.0 CB B:TYR631 4.9 80.2 1.0

M.J.Ammirati, K.M.Andrews, D.D.Boyer, A.M.Brodeur, D.E.Danley, S.D.Doran, B.Hulin, S.Liu, R.K.Mcpherson, S.J.Orena, J.C.Parker, J.Polivkova, X.Qiu, C.B.Soglia, J.L.Treadway, M.A.Vanvolkenburg, D.C.Wilder, D.W.Piotrowski. (3,3-Difluoro-Pyrrolidin-1-Yl)-[(2S,4S)-(4-(4-Pyrimidin-2- Yl-Piperazin-1-Yl)-Pyrrolidin-2-Yl]-Methanone: A Potent, Selective, Orally Active Dipeptidyl Peptidase IV Inhibitor. Bioorg.Med.Chem.Lett. V. 19 1991 2009.
ISSN: ISSN 0960-894X
PubMed: 19275964
DOI: 10.1016/J.BMCL.2009.02.041