Fluorine in PDB 2qky: Complex Structure of Dipeptidyl Peptidase IV and A Oxadiazolyl Ketone

All present enzymatic activity of Complex Structure of Dipeptidyl Peptidase IV and A Oxadiazolyl Ketone:
3.4.14.5;

The structure of Complex Structure of Dipeptidyl Peptidase IV and A Oxadiazolyl Ketone, PDB code: 2qky was solved by K.-H.Kim, S.Y.Hong, K.D.Koo, C.-S.Lee, G.T.Kim, H.O.Han, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 3.10
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	73.178, 106.115, 132.051, 76.30, 78.62, 80.11
R / Rfree (%)	21.4 / 29.3

The binding sites of Fluorine atom in the Complex Structure of Dipeptidyl Peptidase IV and A Oxadiazolyl Ketone (pdb code 2qky). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Complex Structure of Dipeptidyl Peptidase IV and A Oxadiazolyl Ketone, PDB code: 2qky:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Complex Structure of Dipeptidyl Peptidase IV and A Oxadiazolyl Ketone


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Complex Structure of Dipeptidyl Peptidase IV and A Oxadiazolyl Ketone within 5.0Å range: probe atom residue distance (Å) B Occ A:F767 b:31.9 occ:1.00 F1 A:13Z767 0.0 31.9 1.0 C3 A:13Z767 1.3 31.9 1.0 C2 A:13Z767 2.3 31.9 1.0 C4 A:13Z767 2.4 31.9 1.0 O2 A:13Z767 2.7 31.9 1.0 CB A:TYR631 2.9 18.4 1.0 CD2 A:TYR631 2.9 18.4 1.0 C1 A:13Z767 3.1 31.9 1.0 N1 A:13Z767 3.2 31.9 1.0 CG A:TYR631 3.3 18.4 1.0 C7 A:13Z767 3.4 31.9 1.0 CA A:TYR631 3.6 15.6 1.0 OH A:TYR666 3.7 44.2 1.0 N A:TYR631 3.8 15.6 1.0 OG A:SER630 4.0 24.2 1.0 OH A:TYR547 4.0 31.7 1.0 CE1 A:TYR666 4.0 44.2 1.0 CZ A:TYR666 4.0 44.2 1.0 CE2 A:TYR631 4.1 18.4 1.0 CH2 A:TRP659 4.3 22.6 1.0 C5 A:13Z767 4.5 31.9 1.0 CG2 A:VAL656 4.6 14.1 1.0 CZ3 A:TRP659 4.6 22.6 1.0 C8 A:13Z767 4.7 31.9 1.0 CD1 A:TYR631 4.7 18.4 1.0 C A:SER630 4.8 27.7 1.0 CD1 A:TYR666 4.9 44.2 1.0 CZ A:TYR547 4.9 31.7 1.0 CE2 A:TYR666 4.9 44.2 1.0 CE2 A:TYR662 5.0 24.4 1.0

Fluorine binding site 2 out of 4 in the Complex Structure of Dipeptidyl Peptidase IV and A Oxadiazolyl Ketone


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Complex Structure of Dipeptidyl Peptidase IV and A Oxadiazolyl Ketone within 5.0Å range: probe atom residue distance (Å) B Occ B:F767 b:31.9 occ:1.00 F1 B:13Z767 0.0 31.9 1.0 C3 B:13Z767 1.3 31.9 1.0 C2 B:13Z767 2.3 31.9 1.0 C4 B:13Z767 2.4 31.9 1.0 O2 B:13Z767 2.6 31.9 1.0 CB B:TYR631 3.0 18.0 1.0 C1 B:13Z767 3.0 31.9 1.0 N1 B:13Z767 3.2 31.9 1.0 C7 B:13Z767 3.3 31.9 1.0 CD2 B:TYR631 3.4 18.0 1.0 CA B:TYR631 3.5 15.4 1.0 N B:TYR631 3.5 15.4 1.0 OH B:TYR666 3.5 33.1 1.0 CG B:TYR631 3.7 18.0 1.0 OH B:TYR547 3.8 24.0 1.0 OG B:SER630 3.8 21.6 1.0 CZ B:TYR666 3.9 33.1 1.0 CE1 B:TYR666 4.4 33.1 1.0 C5 B:13Z767 4.5 31.9 1.0 CE2 B:TYR666 4.5 33.1 1.0 CH2 B:TRP659 4.5 15.6 1.0 C B:SER630 4.6 24.7 1.0 C8 B:13Z767 4.6 31.9 1.0 CG2 B:VAL656 4.7 17.7 1.0 CE2 B:TYR631 4.7 18.0 1.0 CZ B:TYR547 4.7 24.0 1.0 CE2 B:TYR662 4.8 13.3 1.0 CB B:SER630 4.9 21.6 1.0 C B:TYR631 4.9 15.4 1.0

Fluorine binding site 3 out of 4 in the Complex Structure of Dipeptidyl Peptidase IV and A Oxadiazolyl Ketone


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Complex Structure of Dipeptidyl Peptidase IV and A Oxadiazolyl Ketone within 5.0Å range: probe atom residue distance (Å) B Occ C:F767 b:31.9 occ:1.00 F1 C:13Z767 0.0 31.9 1.0 C3 C:13Z767 1.3 31.9 1.0 C2 C:13Z767 2.3 31.9 1.0 C4 C:13Z767 2.3 31.9 1.0 O2 C:13Z767 2.9 31.9 1.0 CB C:TYR631 3.0 23.8 1.0 C1 C:13Z767 3.1 31.9 1.0 N1 C:13Z767 3.2 31.9 1.0 CD2 C:TYR631 3.2 23.8 1.0 C7 C:13Z767 3.5 31.9 1.0 CG C:TYR631 3.6 23.8 1.0 CA C:TYR631 3.6 20.5 1.0 OH C:TYR666 3.8 14.0 1.0 CE1 C:TYR666 3.9 14.0 1.0 N C:TYR631 3.9 20.5 1.0 CZ C:TYR666 4.0 14.0 1.0 OG C:SER630 4.1 26.3 1.0 CH2 C:TRP659 4.2 12.9 1.0 OH C:TYR547 4.3 8.5 1.0 CG2 C:VAL656 4.4 12.3 1.0 CE2 C:TYR631 4.4 23.8 1.0 CZ3 C:TRP659 4.4 12.9 1.0 C5 C:13Z767 4.5 31.9 1.0 CD1 C:TYR666 4.7 14.0 1.0 C8 C:13Z767 4.8 31.9 1.0 C C:SER630 4.9 23.4 1.0 CE2 C:TYR666 4.9 14.0 1.0 CD1 C:TYR631 4.9 23.8 1.0 CZ C:TYR662 5.0 24.3 1.0

Fluorine binding site 4 out of 4 in the Complex Structure of Dipeptidyl Peptidase IV and A Oxadiazolyl Ketone


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Complex Structure of Dipeptidyl Peptidase IV and A Oxadiazolyl Ketone within 5.0Å range: probe atom residue distance (Å) B Occ D:F767 b:31.9 occ:1.00 F1 D:13Z767 0.0 31.9 1.0 C3 D:13Z767 1.3 31.9 1.0 C2 D:13Z767 2.3 31.9 1.0 C4 D:13Z767 2.3 31.9 1.0 O2 D:13Z767 2.7 31.9 1.0 CB D:TYR631 2.9 32.8 1.0 CD2 D:TYR631 3.0 32.8 1.0 C1 D:13Z767 3.1 31.9 1.0 N1 D:13Z767 3.2 31.9 1.0 CG D:TYR631 3.4 32.8 1.0 C7 D:13Z767 3.4 31.9 1.0 CA D:TYR631 3.6 14.0 1.0 OH D:TYR666 3.7 13.7 1.0 N D:TYR631 3.8 14.0 1.0 OH D:TYR547 4.0 12.1 1.0 OG D:SER630 4.0 24.3 1.0 CZ D:TYR666 4.1 13.7 1.0 CE1 D:TYR666 4.1 13.7 1.0 CE2 D:TYR631 4.3 32.8 1.0 CH2 D:TRP659 4.4 16.6 1.0 CG2 D:VAL656 4.4 22.8 1.0 C5 D:13Z767 4.5 31.9 1.0 C D:SER630 4.6 38.5 1.0 CZ3 D:TRP659 4.7 16.6 1.0 C8 D:13Z767 4.8 31.9 1.0 CD1 D:TYR631 4.8 32.8 1.0 CE2 D:TYR666 4.9 13.7 1.0 CZ D:TYR547 4.9 12.1 1.0

K.D.Koo, M.J.Kim, S.Kim, K.H.Kim, S.Y.Hong, G.C.Hur, H.J.Yim, G.T.Kim, H.O.Han, O.H.Kwon, T.S.Kwon, J.S.Koh, C.S.Lee. Synthesis, Sar, and X-Ray Structure of Novel Potent Dppiv Inhibitors: Oxadiazolyl Ketones. Bioorg.Med.Chem.Lett. V. 17 4167 2007.
ISSN: ISSN 0960-894X
PubMed: 17544668
DOI: 10.1016/J.BMCL.2007.05.046