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Fluorine in PDB 3vjl: Crystal Structure of Human Depiptidyl Peptidase IV (Dpp-4) in Complex with A Prolylthiazolidine Inhibitor #2

Enzymatic activity of Crystal Structure of Human Depiptidyl Peptidase IV (Dpp-4) in Complex with A Prolylthiazolidine Inhibitor #2

All present enzymatic activity of Crystal Structure of Human Depiptidyl Peptidase IV (Dpp-4) in Complex with A Prolylthiazolidine Inhibitor #2:
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 #2, PDB code: 3vjl 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 / 2.39
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 117.810, 125.830, 137.129, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 23

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 #2 (pdb code 3vjl). 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 #2, PDB code: 3vjl:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3vjl

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


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 #2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1000

b:52.9
occ:1.00
 F13 A:W941000 0.0 52.9 1.0
C12 A:W941000 1.3 52.3 1.0
F15 A:W941000 2.2 53.6 1.0
F14 A:W941000 2.2 53.7 1.0
C3 A:W941000 2.3 48.8 1.0
N4 A:W941000 2.7 47.4 1.0
C2 A:W941000 3.6 45.6 1.0
N5 A:W941000 4.0 44.2 1.0
C1 A:W941000 4.4 41.4 1.0
O A:HOH2114 4.9 30.2 1.0
C6 A:W941000 4.9 44.6 1.0
OH A:TYR585 5.0 19.9 1.0

Fluorine binding site 2 out of 6 in 3vjl

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


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 #2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1000

b:53.7
occ:1.00
 F14 A:W941000 0.0 53.7 1.0
C12 A:W941000 1.3 52.3 1.0
F15 A:W941000 2.2 53.6 1.0
F13 A:W941000 2.2 52.9 1.0
C3 A:W941000 2.3 48.8 1.0
C2 A:W941000 2.8 45.6 1.0
N4 A:W941000 3.5 47.4 1.0
C1 A:W941000 4.1 41.4 1.0
N5 A:W941000 4.4 44.2 1.0
O A:HOH2276 4.8 26.3 1.0
O A:HOH2239 4.9 26.8 1.0

Fluorine binding site 3 out of 6 in 3vjl

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


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 #2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1000

b:53.6
occ:1.00
 F15 A:W941000 0.0 53.6 1.0
C12 A:W941000 1.3 52.3 1.0
F13 A:W941000 2.2 52.9 1.0
F14 A:W941000 2.2 53.7 1.0
C3 A:W941000 2.3 48.8 1.0
N4 A:W941000 3.0 47.4 1.0
C2 A:W941000 3.2 45.6 1.0
N5 A:W941000 4.1 44.2 1.0
C1 A:W941000 4.3 41.4 1.0

Fluorine binding site 4 out of 6 in 3vjl

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


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 #2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1000

b:53.3
occ:1.00
 F13 B:W941000 0.0 53.3 1.0
C12 B:W941000 1.3 53.1 1.0
F14 B:W941000 2.1 54.2 1.0
F15 B:W941000 2.2 52.4 1.0
C3 B:W941000 2.3 50.9 1.0
N4 B:W941000 2.7 49.4 1.0
C2 B:W941000 3.6 47.8 1.0
N5 B:W941000 4.0 47.0 1.0
C1 B:W941000 4.5 44.8 1.0
C6 B:W941000 5.0 47.5 1.0

Fluorine binding site 5 out of 6 in 3vjl

Go back to Fluorine Binding Sites List in 3vjl
Fluorine binding site 5 out of 6 in the Crystal Structure of Human Depiptidyl Peptidase IV (Dpp-4) in Complex with A Prolylthiazolidine Inhibitor #2


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 #2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1000

b:54.2
occ:1.00
 F14 B:W941000 0.0 54.2 1.0
C12 B:W941000 1.3 53.1 1.0
F13 B:W941000 2.1 53.3 1.0
F15 B:W941000 2.2 52.4 1.0
C3 B:W941000 2.4 50.9 1.0
C2 B:W941000 2.9 47.8 1.0
N4 B:W941000 3.5 49.4 1.0
C1 B:W941000 4.2 44.8 1.0
N5 B:W941000 4.4 47.0 1.0

Fluorine binding site 6 out of 6 in 3vjl

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


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 #2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1000

b:52.4
occ:1.00
 F15 B:W941000 0.0 52.4 1.0
C12 B:W941000 1.3 53.1 1.0
F14 B:W941000 2.2 54.2 1.0
F13 B:W941000 2.2 53.3 1.0
C3 B:W941000 2.3 50.9 1.0
N4 B:W941000 3.2 49.4 1.0
C2 B:W941000 3.2 47.8 1.0
N5 B:W941000 4.2 47.0 1.0
C1 B:W941000 4.3 44.8 1.0

Reference:

T.Yoshida, F.Akahoshi, H.Sakashita, H.Kitajima, M.Nakamura, S.Sonda, M.Takeuchi, Y.Tanaka, N.Ueda, S.Sekiguchi, T.Ishige, K.Shima, M.Nabeno, Y.Abe, J.Anabuki, A.Soejima, K.Yoshida, Y.Takashina, S.Ishii, S.Kiuchi, S.Fukuda, R.Tsutsumiuchi, K.Kosaka, T.Murozono, Y.Nakamaru, H.Utsumi, N.Masutomi, H.Kishida, I.Miyaguchi, Y.Hayashi. Discovery and Preclinical Profile of Teneligliptin (3-[(2S,4S)-4-[4-(3-Methyl-1-Phenyl-1H-Pyrazol-5-Yl) Piperazin-1-Yl]Pyrrolidin-2-Ylcarbonyl]Thiazolidine): A Highly Potent, Selective, Long-Lasting and Orally Active Dipeptidyl Peptidase IV Inhibitor For the Treatment of Type 2 Diabetes Bioorg.Med.Chem. V. 20 5705 2012.
ISSN: ISSN 0968-0896
PubMed: 22959556
DOI: 10.1016/J.BMC.2012.08.012
Page generated: Sun Dec 13 11:57:04 2020

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