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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

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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

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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

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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

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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

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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

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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

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