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Fluorine in PDB 2qjr: Dipepdyl Peptidase IV in Complex with Inhibitor Pzf

Enzymatic activity of Dipepdyl Peptidase IV in Complex with Inhibitor Pzf

All present enzymatic activity of Dipepdyl Peptidase IV in Complex with Inhibitor Pzf:
3.4.14.5;

Protein crystallography data

The structure of Dipepdyl Peptidase IV in Complex with Inhibitor Pzf, PDB code: 2qjr was solved by L.Shenping, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.90 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.470, 68.796, 422.611, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 25.3

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Dipepdyl Peptidase IV in Complex with Inhibitor Pzf (pdb code 2qjr). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Dipepdyl Peptidase IV in Complex with Inhibitor Pzf, PDB code: 2qjr:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 2qjr

Go back to Fluorine Binding Sites List in 2qjr
Fluorine binding site 1 out of 6 in the Dipepdyl Peptidase IV in Complex with Inhibitor Pzf


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Dipepdyl Peptidase IV in Complex with Inhibitor Pzf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F900

b:54.0
occ:1.00
 F29 A:PZF900 0.0 54.0 1.0
C24 A:PZF900 1.3 50.6 1.0
C23 A:PZF900 2.3 49.2 1.0
C25 A:PZF900 2.4 49.1 1.0
F28 A:PZF900 2.8 52.1 1.0
CG2 A:VAL656 3.3 50.9 1.0
CG2 A:VAL711 3.3 47.6 1.0
C26 A:PZF900 3.6 50.5 1.0
C22 A:PZF900 3.6 49.0 1.0
C A:SER630 3.7 50.6 1.0
N A:TYR631 3.7 50.9 1.0
CB A:SER630 3.7 54.2 1.0
CA A:SER630 3.9 51.6 1.0
C21 A:PZF900 4.1 49.0 1.0
O A:SER630 4.1 50.6 1.0
OG A:SER630 4.2 58.6 1.0
CA A:TYR631 4.3 49.4 1.0
CZ A:TYR662 4.4 50.6 1.0
CE1 A:TYR662 4.5 49.4 1.0
CB A:VAL656 4.6 51.2 1.0
NE2 A:HIS740 4.6 48.2 1.0
CB A:VAL711 4.6 48.8 1.0
OH A:TYR662 4.7 51.5 1.0
CB A:TYR631 4.7 49.2 1.0
F27 A:PZF900 4.7 44.4 1.0
CE1 A:HIS740 4.7 55.1 1.0
CE2 A:TYR662 4.7 50.3 1.0
N A:VAL656 4.8 50.9 1.0
CG1 A:VAL711 4.9 48.6 1.0
CD1 A:TYR662 4.9 49.0 1.0
O A:ALA654 4.9 49.6 1.0

Fluorine binding site 2 out of 6 in 2qjr

Go back to Fluorine Binding Sites List in 2qjr
Fluorine binding site 2 out of 6 in the Dipepdyl Peptidase IV in Complex with Inhibitor Pzf


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Dipepdyl Peptidase IV in Complex with Inhibitor Pzf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F900

b:44.4
occ:1.00
 F27 A:PZF900 0.0 44.4 1.0
C22 A:PZF900 1.3 49.0 1.0
C21 A:PZF900 2.3 49.0 1.0
C23 A:PZF900 2.4 49.2 1.0
C13 A:PZF900 2.8 51.0 1.0
ND2 A:ASN710 3.1 51.1 1.0
O A:HOH975 3.3 54.7 1.0
NH2 A:ARG125 3.4 59.3 1.0
OE2 A:GLU205 3.4 59.0 1.0
C26 A:PZF900 3.6 50.5 1.0
OH A:TYR662 3.6 51.5 1.0
C24 A:PZF900 3.6 50.6 1.0
N20 A:PZF900 3.7 49.5 1.0
C17 A:PZF900 3.8 52.4 1.0
CG A:ASN710 3.8 48.8 1.0
OD1 A:ASN710 3.9 52.6 1.0
C14 A:PZF900 4.0 57.2 1.0
C25 A:PZF900 4.1 49.1 1.0
CD2 A:HIS740 4.1 52.8 1.0
NE2 A:HIS740 4.1 48.2 1.0
OG A:SER630 4.4 58.6 1.0
CD A:GLU205 4.6 57.3 1.0
CZ A:ARG125 4.6 59.5 1.0
F29 A:PZF900 4.7 54.0 1.0
CZ A:TYR662 4.8 50.6 1.0
N15 A:PZF900 4.8 60.2 1.0
C16 A:PZF900 4.9 57.6 1.0
CB A:ASN710 5.0 46.7 1.0

Fluorine binding site 3 out of 6 in 2qjr

Go back to Fluorine Binding Sites List in 2qjr
Fluorine binding site 3 out of 6 in the Dipepdyl Peptidase IV in Complex with Inhibitor Pzf


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Dipepdyl Peptidase IV in Complex with Inhibitor Pzf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F900

b:52.1
occ:1.00
 F28 A:PZF900 0.0 52.1 1.0
C25 A:PZF900 1.3 49.1 1.0
C26 A:PZF900 2.3 50.5 1.0
C24 A:PZF900 2.4 50.6 1.0
F29 A:PZF900 2.8 54.0 1.0
CD2 A:TYR631 3.4 49.0 1.0
CE1 A:TYR666 3.6 47.7 1.0
C21 A:PZF900 3.6 49.0 1.0
OH A:TYR666 3.6 50.9 1.0
CZ A:TYR666 3.7 50.6 1.0
C23 A:PZF900 3.7 49.2 1.0
CB A:TYR631 3.7 49.2 1.0
CH2 A:TRP659 3.8 51.0 1.0
CG A:TYR631 4.0 50.1 1.0
C22 A:PZF900 4.1 49.0 1.0
CZ3 A:TRP659 4.1 50.8 1.0
CA A:TYR631 4.2 49.4 1.0
CE2 A:TYR662 4.2 50.3 1.0
CD1 A:TYR666 4.3 47.0 1.0
N A:TYR631 4.4 50.9 1.0
CE2 A:TYR631 4.4 50.8 1.0
CG2 A:VAL656 4.5 50.9 1.0
CE2 A:TYR666 4.5 49.9 1.0
CD2 A:TYR662 4.7 49.2 1.0
CZ A:TYR662 4.7 50.6 1.0
C13 A:PZF900 4.8 51.0 1.0
OH A:TYR662 4.9 51.5 1.0
OH A:TYR547 5.0 63.5 1.0

Fluorine binding site 4 out of 6 in 2qjr

Go back to Fluorine Binding Sites List in 2qjr
Fluorine binding site 4 out of 6 in the Dipepdyl Peptidase IV in Complex with Inhibitor Pzf


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Dipepdyl Peptidase IV in Complex with Inhibitor Pzf within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F900

b:44.8
occ:1.00
 F29 B:PZF900 0.0 44.8 1.0
C24 B:PZF900 1.3 41.6 1.0
C23 B:PZF900 2.3 38.2 1.0
C25 B:PZF900 2.3 39.6 1.0
F28 B:PZF900 2.7 42.7 1.0
OG B:SER630 3.3 56.2 1.0
CG2 B:VAL711 3.4 48.1 1.0
CG2 B:VAL656 3.4 51.0 1.0
C22 B:PZF900 3.5 42.1 1.0
C26 B:PZF900 3.5 35.5 1.0
C B:SER630 3.9 49.8 1.0
N B:TYR631 3.9 50.8 1.0
C21 B:PZF900 4.0 39.2 1.0
CA B:SER630 4.2 51.2 1.0
CE1 B:TYR662 4.2 48.2 1.0
CB B:SER630 4.3 52.8 1.0
CZ B:TYR662 4.3 48.3 1.0
O B:SER630 4.4 50.3 1.0
CA B:TYR631 4.5 49.5 1.0
NE2 B:HIS740 4.5 54.8 1.0
OH B:TYR662 4.5 52.6 1.0
CB B:VAL656 4.6 53.3 1.0
CE1 B:HIS740 4.6 57.7 1.0
F27 B:PZF900 4.6 45.4 1.0
CD1 B:TYR662 4.6 44.7 1.0
CB B:VAL711 4.7 45.7 1.0
N B:VAL656 4.8 51.5 1.0
CE2 B:TYR662 4.9 48.5 1.0
CG1 B:VAL711 4.9 51.5 1.0
CB B:TYR631 5.0 49.9 1.0
O B:ALA654 5.0 49.1 1.0

Fluorine binding site 5 out of 6 in 2qjr

Go back to Fluorine Binding Sites List in 2qjr
Fluorine binding site 5 out of 6 in the Dipepdyl Peptidase IV in Complex with Inhibitor Pzf


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Dipepdyl Peptidase IV in Complex with Inhibitor Pzf within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F900

b:45.4
occ:1.00
 F27 B:PZF900 0.0 45.4 1.0
C22 B:PZF900 1.3 42.1 1.0
C21 B:PZF900 2.3 39.2 1.0
C23 B:PZF900 2.3 38.2 1.0
C13 B:PZF900 2.8 43.3 1.0
NH2 B:ARG125 3.2 59.7 1.0
ND2 B:ASN710 3.3 49.5 1.0
O B:HOH914 3.4 46.7 1.0
C26 B:PZF900 3.5 35.5 1.0
C24 B:PZF900 3.6 41.6 1.0
OE2 B:GLU205 3.6 49.5 1.0
N20 B:PZF900 3.7 37.0 1.0
OH B:TYR662 3.7 52.6 1.0
C17 B:PZF900 3.7 40.5 1.0
NE2 B:HIS740 3.8 54.8 1.0
CG B:ASN710 3.8 49.4 1.0
CD2 B:HIS740 3.8 56.8 1.0
OD1 B:ASN710 3.8 51.0 1.0
OG B:SER630 4.0 56.2 1.0
C25 B:PZF900 4.0 39.6 1.0
C14 B:PZF900 4.0 45.8 1.0
CZ B:ARG125 4.5 60.2 1.0
F29 B:PZF900 4.6 44.8 1.0
C16 B:PZF900 4.7 44.5 1.0
CD B:GLU205 4.7 55.8 1.0
CZ B:TYR662 4.8 48.3 1.0
CE1 B:HIS740 4.9 57.7 1.0
N15 B:PZF900 4.9 44.3 1.0
CG B:HIS740 4.9 55.2 1.0

Fluorine binding site 6 out of 6 in 2qjr

Go back to Fluorine Binding Sites List in 2qjr
Fluorine binding site 6 out of 6 in the Dipepdyl Peptidase IV in Complex with Inhibitor Pzf


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Dipepdyl Peptidase IV in Complex with Inhibitor Pzf within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F900

b:42.7
occ:1.00
 F28 B:PZF900 0.0 42.7 1.0
C25 B:PZF900 1.3 39.6 1.0
C24 B:PZF900 2.3 41.6 1.0
C26 B:PZF900 2.3 35.5 1.0
F29 B:PZF900 2.7 44.8 1.0
CD2 B:TYR631 3.5 51.5 1.0
C23 B:PZF900 3.6 38.2 1.0
C21 B:PZF900 3.6 39.2 1.0
CE1 B:TYR666 3.6 48.7 1.0
OH B:TYR666 3.6 49.8 1.0
CZ B:TYR666 3.7 50.1 1.0
CB B:TYR631 3.9 49.9 1.0
CH2 B:TRP659 3.9 49.8 1.0
C22 B:PZF900 4.0 42.1 1.0
CG B:TYR631 4.1 51.4 1.0
CA B:TYR631 4.2 49.5 1.0
CZ3 B:TRP659 4.2 49.5 1.0
N B:TYR631 4.3 50.8 1.0
CE2 B:TYR631 4.4 54.4 1.0
CD1 B:TYR666 4.4 47.4 1.0
CE2 B:TYR662 4.4 48.5 1.0
CG2 B:VAL656 4.6 51.0 1.0
CE2 B:TYR666 4.6 47.8 1.0
OG B:SER630 4.6 56.2 1.0
CZ B:TYR662 4.6 48.3 1.0
OH B:TYR547 4.7 57.2 1.0
C13 B:PZF900 4.8 43.3 1.0
CD2 B:TYR662 4.8 44.3 1.0
OH B:TYR662 4.9 52.6 1.0

Reference:

W.Stephen, A.Mark, A.Kim, B.Anne, D.Dennis, L.Jay, L.Shenping, M.Lester, M.Kik, O.Thanh. (3R,4S)-4-(2,4,5-Trifluorophenyl)-Pyrrolidin-3-Ylamine Inhibitors of Dipeptidyl Peptidase IV: Synthesis, in Vitro, in Vivo and X-Ray Crystallographic Characterization To Be Published.
Page generated: Wed Jul 31 15:47:21 2024

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