Atomistry » Fluorine » PDB 3uyt-3vrb » 3vjm
Atomistry »
  Fluorine »
    PDB 3uyt-3vrb »
      3vjm »

Fluorine in PDB 3vjm: Crystal Structure of Human Depiptidyl Peptidase IV (Dpp-4) in Complex with A Prolylthiazolidine Inhibitor #1

Enzymatic activity of Crystal Structure of Human Depiptidyl Peptidase IV (Dpp-4) in Complex with A Prolylthiazolidine Inhibitor #1

All present enzymatic activity of Crystal Structure of Human Depiptidyl Peptidase IV (Dpp-4) in Complex with A Prolylthiazolidine Inhibitor #1:
3.4.14.5;

Protein crystallography data

The structure of Crystal Structure of Human Depiptidyl Peptidase IV (Dpp-4) in Complex with A Prolylthiazolidine Inhibitor #1, PDB code: 3vjm was solved by F.Akahoshi, H.Kishida, I.Miyaguchi, T.Yoshida, S.Ishii, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 117.946, 125.944, 137.214, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 22.4

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Depiptidyl Peptidase IV (Dpp-4) in Complex with A Prolylthiazolidine Inhibitor #1 (pdb code 3vjm). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Human Depiptidyl Peptidase IV (Dpp-4) in Complex with A Prolylthiazolidine Inhibitor #1, PDB code: 3vjm:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3vjm

Go back to Fluorine Binding Sites List in 3vjm
Fluorine binding site 1 out of 6 in the Crystal Structure of Human Depiptidyl Peptidase IV (Dpp-4) in Complex with A Prolylthiazolidine Inhibitor #1


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 Human Depiptidyl Peptidase IV (Dpp-4) in Complex with A Prolylthiazolidine Inhibitor #1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1000

b:40.9
occ:1.00
 F52 A:W611000 0.0 40.9 1.0
C11 A:W611000 1.3 39.1 1.0
F54 A:W611000 2.1 41.6 1.0
F53 A:W611000 2.1 38.8 1.0
C3 A:W611000 2.3 36.5 1.0
N4 A:W611000 2.8 35.1 1.0
C2 A:W611000 3.4 31.8 1.0
C5 A:W611000 4.0 34.8 1.0
C1 A:W611000 4.5 30.6 1.0
C6 A:W611000 4.8 32.9 1.0
C10 A:W611000 4.9 34.7 1.0

Fluorine binding site 2 out of 6 in 3vjm

Go back to Fluorine Binding Sites List in 3vjm
Fluorine binding site 2 out of 6 in the Crystal Structure of Human Depiptidyl Peptidase IV (Dpp-4) in Complex with A Prolylthiazolidine Inhibitor #1


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 Human Depiptidyl Peptidase IV (Dpp-4) in Complex with A Prolylthiazolidine Inhibitor #1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1000

b:38.8
occ:1.00
 F53 A:W611000 0.0 38.8 1.0
C11 A:W611000 1.3 39.1 1.0
F52 A:W611000 2.1 40.9 1.0
F54 A:W611000 2.2 41.6 1.0
C3 A:W611000 2.4 36.5 1.0
C2 A:W611000 2.9 31.8 1.0
N4 A:W611000 3.6 35.1 1.0
O A:HOH2120 3.7 25.4 1.0
O A:HOH2243 4.0 26.6 1.0
C1 A:W611000 4.3 30.6 1.0
OH A:TYR585 4.5 25.3 1.0
C5 A:W611000 4.7 34.8 1.0

Fluorine binding site 3 out of 6 in 3vjm

Go back to Fluorine Binding Sites List in 3vjm
Fluorine binding site 3 out of 6 in the Crystal Structure of Human Depiptidyl Peptidase IV (Dpp-4) in Complex with A Prolylthiazolidine Inhibitor #1


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 Human Depiptidyl Peptidase IV (Dpp-4) in Complex with A Prolylthiazolidine Inhibitor #1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1000

b:41.6
occ:1.00
 F54 A:W611000 0.0 41.6 1.0
C11 A:W611000 1.3 39.1 1.0
F52 A:W611000 2.1 40.9 1.0
F53 A:W611000 2.2 38.8 1.0
C3 A:W611000 2.3 36.5 1.0
N4 A:W611000 2.7 35.1 1.0
OH A:TYR585 3.1 25.3 1.0
C2 A:W611000 3.5 31.8 1.0
O A:HOH2339 3.7 42.9 1.0
O A:HOH2120 3.7 25.4 1.0
C5 A:W611000 4.0 34.8 1.0
CZ A:TYR585 4.4 22.7 1.0
C1 A:W611000 4.6 30.6 1.0
C6 A:W611000 4.8 32.9 1.0
C10 A:W611000 4.8 34.7 1.0
CE2 A:PHE357 4.8 21.7 1.0

Fluorine binding site 4 out of 6 in 3vjm

Go back to Fluorine Binding Sites List in 3vjm
Fluorine binding site 4 out of 6 in the Crystal Structure of Human Depiptidyl Peptidase IV (Dpp-4) in Complex with A Prolylthiazolidine Inhibitor #1


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 Human Depiptidyl Peptidase IV (Dpp-4) in Complex with A Prolylthiazolidine Inhibitor #1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1000

b:39.3
occ:1.00
 F52 B:W611000 0.0 39.3 1.0
C11 B:W611000 1.3 38.0 1.0
F53 B:W611000 2.1 40.4 1.0
F54 B:W611000 2.1 40.2 1.0
C3 B:W611000 2.3 35.5 1.0
C2 B:W611000 2.8 32.7 1.0
O B:HOH2706 3.1 21.5 1.0
N4 B:W611000 3.4 33.5 1.0
O B:HOH2933 3.8 41.9 1.0
OH B:TYR585 3.8 22.0 1.0
O B:HOH2728 4.0 33.0 1.0
C1 B:W611000 4.2 30.9 1.0
C5 B:W611000 4.6 33.0 1.0
CE1 B:PHE357 4.7 22.1 1.0
O B:HOH2926 4.7 38.3 1.0
C6 B:W611000 4.9 31.9 1.0
CZ B:PHE357 4.9 21.0 1.0

Fluorine binding site 5 out of 6 in 3vjm

Go back to Fluorine Binding Sites List in 3vjm
Fluorine binding site 5 out of 6 in the Crystal Structure of Human Depiptidyl Peptidase IV (Dpp-4) in Complex with A Prolylthiazolidine Inhibitor #1


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 Human Depiptidyl Peptidase IV (Dpp-4) in Complex with A Prolylthiazolidine Inhibitor #1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1000

b:40.4
occ:1.00
 F53 B:W611000 0.0 40.4 1.0
C11 B:W611000 1.3 38.0 1.0
F52 B:W611000 2.1 39.3 1.0
F54 B:W611000 2.1 40.2 1.0
C3 B:W611000 2.2 35.5 1.0
N4 B:W611000 2.5 33.5 1.0
O B:HOH2926 3.2 38.3 1.0
OH B:TYR585 3.5 22.0 1.0
C2 B:W611000 3.5 32.7 1.0
O B:HOH2922 3.8 45.7 1.0
C5 B:W611000 3.8 33.0 1.0
O B:HOH2872 4.1 48.4 1.0
O B:HOH2706 4.2 21.5 1.0
C10 B:W611000 4.6 31.6 1.0
C1 B:W611000 4.6 30.9 1.0
C6 B:W611000 4.7 31.9 1.0
CZ B:TYR585 4.8 18.3 1.0

Fluorine binding site 6 out of 6 in 3vjm

Go back to Fluorine Binding Sites List in 3vjm
Fluorine binding site 6 out of 6 in the Crystal Structure of Human Depiptidyl Peptidase IV (Dpp-4) in Complex with A Prolylthiazolidine Inhibitor #1


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 Human Depiptidyl Peptidase IV (Dpp-4) in Complex with A Prolylthiazolidine Inhibitor #1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1000

b:40.2
occ:1.00
 F54 B:W611000 0.0 40.2 1.0
C11 B:W611000 1.3 38.0 1.0
F53 B:W611000 2.1 40.4 1.0
F52 B:W611000 2.1 39.3 1.0
C3 B:W611000 2.3 35.5 1.0
N4 B:W611000 3.1 33.5 1.0
C2 B:W611000 3.2 32.7 1.0
C5 B:W611000 4.3 33.0 1.0
C1 B:W611000 4.5 30.9 1.0
C6 B:W611000 4.9 31.9 1.0

Reference:

T.Yoshida, F.Akahoshi, H.Sakashita, S.Sonda, M.Takeuchi, Y.Tanaka, M.Nabeno, H.Kishida, I.Miyaguchi, Y.Hayashi. Fused Bicyclic Heteroarylpiperazine-Substituted L-Prolylthiazolidines As Highly Potent Dpp-4 Inhibitors Lacking the Electrophilic Nitrile Group Bioorg.Med.Chem. V. 20 5033 2012.
ISSN: ISSN 0968-0896
PubMed: 22824762
DOI: 10.1016/J.BMC.2012.06.033
Page generated: Mon Jul 14 19:53:58 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy