Fluorine in PDB 5kby: Crystal Structure of Dipeptidyl Peptidase IV in Complex with Syr-472

All present enzymatic activity of Crystal Structure of Dipeptidyl Peptidase IV in Complex with Syr-472:
3.4.14.5;

The structure of Crystal Structure of Dipeptidyl Peptidase IV in Complex with Syr-472, PDB code: 5kby was solved by R.J.Skene, A.J.Jennings, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.57 / 2.24
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	121.573, 122.165, 143.704, 90.00, 114.57, 90.00
R / Rfree (%)	17.4 / 21.5

The binding sites of Fluorine atom in the Crystal Structure of Dipeptidyl Peptidase IV in Complex with Syr-472 (pdb code 5kby). 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 Syr-472, PDB code: 5kby:
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 Syr-472


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 Syr-472 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1510 b:28.7 occ:1.00 F20 A:6RL1510 0.0 28.7 1.0 C19 A:6RL1510 1.3 26.1 1.0 C18 A:6RL1510 2.4 24.3 1.0 C21 A:6RL1510 2.4 24.7 1.0 CG2 A:VAL656 3.2 25.3 1.0 CH2 A:TRP659 3.3 25.7 1.0 CZ3 A:TRP659 3.5 23.3 1.0 C17 A:6RL1510 3.6 27.9 1.0 C22 A:6RL1510 3.6 27.9 1.0 CD1 A:TYR631 3.7 22.0 1.0 CA A:TYR631 3.9 23.5 1.0 N A:TYR631 4.0 23.0 1.0 CB A:VAL656 4.0 24.9 1.0 CB A:TYR631 4.0 22.9 1.0 CE2 A:TYR666 4.1 21.7 1.0 C23 A:6RL1510 4.1 28.7 1.0 CE2 A:TYR662 4.2 22.6 1.0 CG A:TYR631 4.3 23.4 1.0 CD2 A:TYR662 4.3 23.4 1.0 CZ2 A:TRP659 4.5 24.5 1.0 CZ A:TYR662 4.5 21.8 1.0 C A:SER630 4.5 23.1 1.0 CE1 A:TYR631 4.6 24.4 1.0 CD2 A:TYR666 4.6 21.8 1.0 CG A:TYR662 4.7 22.1 1.0 CZ A:TYR666 4.7 22.2 1.0 CG1 A:VAL656 4.7 24.0 1.0 CE3 A:TRP659 4.8 23.5 1.0 OH A:TYR666 4.8 25.8 1.0 C16 A:6RL1510 4.8 26.9 1.0 O A:SER630 4.9 25.1 1.0 CE1 A:TYR662 4.9 22.2 1.0 CD1 A:TYR662 5.0 21.7 1.0

Fluorine binding site 2 out of 4 in the Crystal Structure of Dipeptidyl Peptidase IV in Complex with Syr-472


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 Syr-472 within 5.0Å range: probe atom residue distance (Å) B Occ B:F808 b:33.2 occ:1.00 F20 B:6RL808 0.0 33.2 1.0 C19 B:6RL808 1.3 30.9 1.0 C18 B:6RL808 2.3 31.2 1.0 C21 B:6RL808 2.4 31.0 1.0 CG2 B:VAL656 3.1 32.0 1.0 CH2 B:TRP659 3.3 29.1 1.0 CZ3 B:TRP659 3.5 28.6 1.0 C17 B:6RL808 3.6 29.0 1.0 C22 B:6RL808 3.6 30.9 1.0 CD1 B:TYR631 3.7 29.9 1.0 CA B:TYR631 3.9 27.5 1.0 CB B:VAL656 3.9 31.8 1.0 N B:TYR631 4.0 28.2 1.0 CE2 B:TYR666 4.0 28.7 1.0 CB B:TYR631 4.1 29.5 1.0 C23 B:6RL808 4.1 31.2 1.0 CE2 B:TYR662 4.2 28.3 1.0 CD2 B:TYR662 4.2 30.2 1.0 CG B:TYR631 4.3 30.3 1.0 C B:SER630 4.5 27.4 1.0 CZ2 B:TRP659 4.5 32.6 1.0 CE1 B:TYR631 4.6 31.0 1.0 CZ B:TYR662 4.6 28.2 1.0 CD2 B:TYR666 4.6 28.4 1.0 CZ B:TYR666 4.6 27.5 1.0 OH B:TYR666 4.7 26.5 1.0 CG1 B:VAL656 4.7 31.5 1.0 CG B:TYR662 4.7 28.5 1.0 C16 B:6RL808 4.8 26.6 1.0 O B:SER630 4.8 29.7 1.0 CE3 B:TRP659 4.8 29.3 1.0

Fluorine binding site 3 out of 4 in the Crystal Structure of Dipeptidyl Peptidase IV in Complex with Syr-472


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 Syr-472 within 5.0Å range: probe atom residue distance (Å) B Occ C:F1506 b:34.8 occ:1.00 F20 C:6RL1506 0.0 34.8 1.0 C19 C:6RL1506 1.4 31.8 1.0 C18 C:6RL1506 2.4 29.9 1.0 C21 C:6RL1506 2.4 30.9 1.0 CG2 C:VAL656 3.1 36.3 1.0 CH2 C:TRP659 3.3 32.8 1.0 CZ3 C:TRP659 3.5 31.6 1.0 C17 C:6RL1506 3.6 26.8 1.0 C22 C:6RL1506 3.6 27.0 1.0 CD1 C:TYR631 3.6 35.5 1.0 CA C:TYR631 3.8 32.1 1.0 CE2 C:TYR666 4.0 32.9 1.0 N C:TYR631 4.0 34.4 1.0 CB C:TYR631 4.0 33.8 1.0 CB C:VAL656 4.0 33.7 1.0 C23 C:6RL1506 4.1 27.1 1.0 CE2 C:TYR662 4.1 29.3 1.0 CG C:TYR631 4.2 33.6 1.0 CD2 C:TYR662 4.2 31.4 1.0 C C:SER630 4.4 30.7 1.0 CZ2 C:TRP659 4.4 33.0 1.0 CZ C:TYR662 4.5 26.4 1.0 CD2 C:TYR666 4.6 33.9 1.0 CE1 C:TYR631 4.6 37.4 1.0 CZ C:TYR666 4.6 31.5 1.0 O C:SER630 4.7 31.7 1.0 CG C:TYR662 4.7 30.2 1.0 OH C:TYR666 4.7 32.2 1.0 C16 C:6RL1506 4.8 27.2 1.0 CE3 C:TRP659 4.8 32.0 1.0 CG1 C:VAL656 4.9 35.3 1.0 CE1 C:TYR662 5.0 26.4 1.0

Fluorine binding site 4 out of 4 in the Crystal Structure of Dipeptidyl Peptidase IV in Complex with Syr-472


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 Syr-472 within 5.0Å range: probe atom residue distance (Å) B Occ D:F1507 b:27.7 occ:1.00 F20 D:6RL1507 0.0 27.7 1.0 C19 D:6RL1507 1.3 25.6 1.0 C18 D:6RL1507 2.3 25.0 1.0 C21 D:6RL1507 2.4 26.0 1.0 CH2 D:TRP659 3.3 27.3 1.0 CG2 D:VAL656 3.3 27.4 1.0 CD1 D:TYR631 3.5 26.4 1.0 CZ3 D:TRP659 3.5 26.0 1.0 C17 D:6RL1507 3.6 24.2 1.0 C22 D:6RL1507 3.6 25.4 1.0 CA D:TYR631 3.7 25.5 1.0 N D:TYR631 3.8 24.5 1.0 CB D:TYR631 3.8 24.4 1.0 CE2 D:TYR666 4.0 26.8 1.0 CG D:TYR631 4.0 25.6 1.0 C23 D:6RL1507 4.1 24.1 1.0 CB D:VAL656 4.1 27.2 1.0 CE2 D:TYR662 4.4 27.1 1.0 CE1 D:TYR631 4.4 26.9 1.0 CZ2 D:TRP659 4.5 26.6 1.0 C D:SER630 4.5 25.1 1.0 CD2 D:TYR662 4.5 26.4 1.0 CZ D:TYR666 4.6 24.9 1.0 OH D:TYR666 4.6 25.0 1.0 CD2 D:TYR666 4.6 26.9 1.0 CZ D:TYR662 4.7 26.4 1.0 C16 D:6RL1507 4.8 27.8 1.0 CE3 D:TRP659 4.8 26.0 1.0 O27 D:6RL1507 4.8 30.8 1.0 CG D:TYR662 4.9 25.0 1.0 O D:SER630 4.9 26.0 1.0 CG1 D:VAL656 4.9 25.9 1.0

C.E.Grimshaw, A.Jennings, R.Kamran, H.Ueno, N.Nishigaki, T.Kosaka, A.Tani, H.Sano, Y.Kinugawa, E.Koumura, L.Shi, K.Takeuchi. Trelagliptin (Syr-472, Zafatek), Novel Once-Weekly Treatment For Type 2 Diabetes, Inhibits Dipeptidyl Peptidase-4 (Dpp-4) Via A Non-Covalent Mechanism. Plos One V. 11 57509 2016.
ISSN: ESSN 1932-6203
PubMed: 27328054
DOI: 10.1371/JOURNAL.PONE.0157509