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Fluorine in PDB 2qoe: Human Dipeptidyl Peptidase IV in Complex with A Triazolopiperazine- Based Beta Amino Acid Inhibitor

Enzymatic activity of Human Dipeptidyl Peptidase IV in Complex with A Triazolopiperazine- Based Beta Amino Acid Inhibitor

All present enzymatic activity of Human Dipeptidyl Peptidase IV in Complex with A Triazolopiperazine- Based Beta Amino Acid Inhibitor:
3.4.14.5;

Protein crystallography data

The structure of Human Dipeptidyl Peptidase IV in Complex with A Triazolopiperazine- Based Beta Amino Acid Inhibitor, PDB code: 2qoe was solved by G.Scapin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 118.126, 125.296, 136.832, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 21.2

Other elements in 2qoe:

The structure of Human Dipeptidyl Peptidase IV in Complex with A Triazolopiperazine- Based Beta Amino Acid Inhibitor also contains other interesting chemical elements:

Sodium (Na) 1 atom

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Fluorine atom in the Human Dipeptidyl Peptidase IV in Complex with A Triazolopiperazine- Based Beta Amino Acid Inhibitor (pdb code 2qoe). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Human Dipeptidyl Peptidase IV in Complex with A Triazolopiperazine- Based Beta Amino Acid Inhibitor, PDB code: 2qoe:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 2qoe

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Fluorine binding site 1 out of 12 in the Human Dipeptidyl Peptidase IV in Complex with A Triazolopiperazine- Based Beta Amino Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human Dipeptidyl Peptidase IV in Complex with A Triazolopiperazine- Based Beta Amino Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1282

b:21.2
occ:1.00
 F9 A:4481282 0.0 21.2 1.0
C6 A:4481282 1.3 21.0 1.0
C1 A:4481282 2.4 20.1 1.0
C5 A:4481282 2.4 19.9 1.0
F8 A:4481282 2.7 20.0 1.0
CG2 A:VAL656 3.2 23.0 1.0
CG2 A:VAL711 3.3 23.6 1.0
OG A:SER630 3.4 27.3 0.7
C2 A:4481282 3.6 18.1 1.0
C4 A:4481282 3.7 17.8 1.0
N A:TYR631 3.8 26.5 1.0
C A:SER630 3.8 26.2 1.0
CA A:SER630 4.0 25.8 1.0
CB A:SER630 4.1 25.6 0.3
CE1 A:TYR662 4.1 24.0 1.0
C3 A:4481282 4.2 18.9 1.0
CB A:SER630 4.2 25.8 0.7
CZ A:TYR662 4.2 23.5 1.0
O A:SER630 4.3 26.9 1.0
CB A:VAL656 4.3 24.2 1.0
CA A:TYR631 4.4 26.0 1.0
OH A:TYR662 4.4 23.6 1.0
CD1 A:TYR662 4.6 23.5 1.0
NE2 A:HIS740 4.6 26.1 1.0
CB A:VAL711 4.6 24.0 1.0
N A:VAL656 4.7 24.4 1.0
CE1 A:HIS740 4.7 26.1 1.0
F10 A:4481282 4.7 20.0 1.0
CE2 A:TYR662 4.8 23.3 1.0
O A:ALA654 4.9 24.9 1.0
CG1 A:VAL711 4.9 23.8 1.0
CB A:TYR631 4.9 26.1 1.0

Fluorine binding site 2 out of 12 in 2qoe

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Fluorine binding site 2 out of 12 in the Human Dipeptidyl Peptidase IV in Complex with A Triazolopiperazine- Based Beta Amino Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human Dipeptidyl Peptidase IV in Complex with A Triazolopiperazine- Based Beta Amino Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1282

b:20.0
occ:1.00
 F10 A:4481282 0.0 20.0 1.0
C2 A:4481282 1.3 18.1 1.0
C1 A:4481282 2.3 20.1 1.0
C3 A:4481282 2.4 18.9 1.0
C11 A:4481282 2.9 18.1 1.0
ND2 A:ASN710 3.1 24.4 1.0
NH2 A:ARG125 3.1 27.2 1.0
OE2 A:GLU205 3.4 25.9 1.0
CG A:ASN710 3.6 25.8 1.0
O A:HOH1602 3.6 30.4 1.0
OH A:TYR662 3.6 23.6 1.0
C6 A:4481282 3.6 21.0 1.0
N20 A:4481282 3.6 16.3 1.0
OD1 A:ASN710 3.6 27.1 1.0
C4 A:4481282 3.7 17.8 1.0
O A:HOH1663 3.7 43.5 1.0
CD2 A:HIS740 3.7 26.3 1.0
NE2 A:HIS740 3.8 26.1 1.0
OG A:SER630 3.8 27.3 0.7
C12 A:4481282 3.9 19.2 1.0
C5 A:4481282 4.1 19.9 1.0
CZ A:ARG125 4.4 27.6 1.0
CD A:GLU205 4.5 26.5 1.0
F9 A:4481282 4.7 21.2 1.0
CB A:ASN710 4.7 24.7 1.0
CG A:HIS740 4.8 27.5 1.0
CZ A:TYR662 4.8 23.5 1.0
CE1 A:HIS740 4.8 26.1 1.0
OG A:SER630 4.8 24.3 0.3
O A:HOH1312 4.9 15.8 1.0
C15 A:4481282 5.0 21.1 1.0

Fluorine binding site 3 out of 12 in 2qoe

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Fluorine binding site 3 out of 12 in the Human Dipeptidyl Peptidase IV in Complex with A Triazolopiperazine- Based Beta Amino Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human Dipeptidyl Peptidase IV in Complex with A Triazolopiperazine- Based Beta Amino Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1282

b:20.0
occ:1.00
 F8 A:4481282 0.0 20.0 1.0
C5 A:4481282 1.3 19.9 1.0
C6 A:4481282 2.4 21.0 1.0
C4 A:4481282 2.4 17.8 1.0
F9 A:4481282 2.7 21.2 1.0
CD2 A:TYR631 3.3 26.8 1.0
CB A:TYR631 3.5 26.1 1.0
C1 A:4481282 3.7 20.1 1.0
OH A:TYR666 3.7 28.3 1.0
C3 A:4481282 3.7 18.9 1.0
CE1 A:TYR666 3.7 25.8 1.0
CZ A:TYR666 3.8 26.5 1.0
CA A:TYR631 3.8 26.0 1.0
CG A:TYR631 3.8 26.4 1.0
N A:TYR631 3.9 26.5 1.0
CH2 A:TRP659 4.0 23.2 1.0
C2 A:4481282 4.1 18.1 1.0
OH A:TYR547 4.3 27.4 1.0
CZ3 A:TRP659 4.4 24.4 1.0
CE2 A:TYR631 4.4 24.4 1.0
CG2 A:VAL656 4.5 23.0 1.0
CD1 A:TYR666 4.5 25.6 1.0
OG A:SER630 4.5 27.3 0.7
CE2 A:TYR662 4.6 23.3 1.0
CE2 A:TYR666 4.6 25.8 1.0
O A:HOH1577 4.7 28.0 1.0
C A:SER630 4.7 26.2 1.0
CZ A:TYR662 4.7 23.5 1.0
OH A:TYR662 4.9 23.6 1.0
C11 A:4481282 5.0 18.1 1.0

Fluorine binding site 4 out of 12 in 2qoe

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Fluorine binding site 4 out of 12 in the Human Dipeptidyl Peptidase IV in Complex with A Triazolopiperazine- Based Beta Amino Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Human Dipeptidyl Peptidase IV in Complex with A Triazolopiperazine- Based Beta Amino Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1282

b:38.5
occ:1.00
 F29 A:4481282 0.0 38.5 1.0
C41 A:4481282 1.3 36.7 1.0
F28 A:4481282 2.1 39.0 1.0
F27 A:4481282 2.2 37.5 1.0
C40 A:4481282 2.3 36.2 1.0
N41 A:4481282 2.8 35.4 1.0
O A:HOH1512 3.5 32.2 1.0
N39 A:4481282 3.5 34.4 1.0
OH A:TYR585 3.9 27.9 1.0
O A:HOH1629 4.0 32.2 1.0
C28 A:4481282 4.1 34.2 1.0
N27 A:4481282 4.4 32.8 1.0
CE2 A:PHE357 4.8 25.9 1.0

Fluorine binding site 5 out of 12 in 2qoe

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Fluorine binding site 5 out of 12 in the Human Dipeptidyl Peptidase IV in Complex with A Triazolopiperazine- Based Beta Amino Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Human Dipeptidyl Peptidase IV in Complex with A Triazolopiperazine- Based Beta Amino Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1282

b:37.5
occ:1.00
 F27 A:4481282 0.0 37.5 1.0
C41 A:4481282 1.3 36.7 1.0
F28 A:4481282 2.2 39.0 1.0
F29 A:4481282 2.2 38.5 1.0
C40 A:4481282 2.3 36.2 1.0
N39 A:4481282 2.6 34.4 1.0
N41 A:4481282 3.5 35.4 1.0
N27 A:4481282 4.0 32.8 1.0
O A:HOH1682 4.2 41.2 1.0
C28 A:4481282 4.3 34.2 1.0
O A:HOH1537 4.6 20.1 1.0
CD2 A:PHE357 4.7 26.2 1.0

Fluorine binding site 6 out of 12 in 2qoe

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Fluorine binding site 6 out of 12 in the Human Dipeptidyl Peptidase IV in Complex with A Triazolopiperazine- Based Beta Amino Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Human Dipeptidyl Peptidase IV in Complex with A Triazolopiperazine- Based Beta Amino Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1282

b:39.0
occ:1.00
 F28 A:4481282 0.0 39.0 1.0
C41 A:4481282 1.3 36.7 1.0
F29 A:4481282 2.1 38.5 1.0
F27 A:4481282 2.2 37.5 1.0
C40 A:4481282 2.4 36.2 1.0
N41 A:4481282 3.2 35.4 1.0
N39 A:4481282 3.3 34.4 1.0
OH A:TYR585 3.4 27.9 1.0
CE2 A:PHE357 3.5 25.9 1.0
CD2 A:PHE357 3.5 26.2 1.0
O A:HOH1629 3.9 32.2 1.0
O A:HOH1512 4.1 32.2 1.0
C28 A:4481282 4.3 34.2 1.0
N27 A:4481282 4.3 32.8 1.0
CZ A:TYR585 4.6 24.8 1.0
CD A:ARG356 4.7 28.1 1.0
O A:HOH1537 4.7 20.1 1.0
CZ A:PHE357 4.7 26.1 1.0
CB A:ARG356 4.8 27.5 1.0
CG A:PHE357 4.8 26.3 1.0
CE1 A:TYR585 5.0 24.0 1.0

Fluorine binding site 7 out of 12 in 2qoe

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Fluorine binding site 7 out of 12 in the Human Dipeptidyl Peptidase IV in Complex with A Triazolopiperazine- Based Beta Amino Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Human Dipeptidyl Peptidase IV in Complex with A Triazolopiperazine- Based Beta Amino Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2

b:21.9
occ:1.00
 F9 B:4482 0.0 21.9 1.0
C6 B:4482 1.3 21.8 1.0
C5 B:4482 2.4 21.6 1.0
C1 B:4482 2.4 20.4 1.0
F8 B:4482 2.7 21.1 1.0
CG2 B:VAL656 3.1 22.5 1.0
CG2 B:VAL711 3.2 24.2 1.0
OG B:SER630 3.2 25.5 0.7
C2 B:4482 3.6 21.1 1.0
C4 B:4482 3.7 21.4 1.0
N B:TYR631 3.8 25.2 1.0
C B:SER630 3.9 25.7 1.0
CE1 B:TYR662 4.1 23.6 1.0
CZ B:TYR662 4.1 24.7 1.0
C3 B:4482 4.2 21.7 1.0
CA B:SER630 4.2 25.6 1.0
CB B:SER630 4.2 25.6 0.3
CB B:SER630 4.2 25.6 0.7
O B:SER630 4.3 26.1 1.0
OH B:TYR662 4.4 26.9 1.0
CB B:VAL656 4.4 24.3 1.0
CA B:TYR631 4.4 24.6 1.0
CD1 B:TYR662 4.5 23.0 1.0
NE2 B:HIS740 4.6 24.7 1.0
CE2 B:TYR662 4.6 21.3 1.0
CB B:VAL711 4.6 25.1 1.0
CE1 B:HIS740 4.7 25.9 1.0
N B:VAL656 4.8 24.2 1.0
F10 B:4482 4.8 20.6 1.0
CB B:TYR631 4.9 24.6 1.0
CG1 B:VAL711 5.0 24.0 1.0
CG B:TYR662 5.0 23.6 1.0

Fluorine binding site 8 out of 12 in 2qoe

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Fluorine binding site 8 out of 12 in the Human Dipeptidyl Peptidase IV in Complex with A Triazolopiperazine- Based Beta Amino Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Human Dipeptidyl Peptidase IV in Complex with A Triazolopiperazine- Based Beta Amino Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2

b:20.6
occ:1.00
 F10 B:4482 0.0 20.6 1.0
C2 B:4482 1.3 21.1 1.0
C1 B:4482 2.4 20.4 1.0
C3 B:4482 2.5 21.7 1.0
C11 B:4482 2.9 20.9 1.0
NH2 B:ARG125 3.0 31.7 1.0
ND2 B:ASN710 3.0 26.9 1.0
OE2 B:GLU205 3.4 31.2 1.0
OH B:TYR662 3.6 26.9 1.0
OD1 B:ASN710 3.6 27.9 1.0
CG B:ASN710 3.6 26.9 1.0
C6 B:4482 3.6 21.8 1.0
O B:HOH2486 3.7 28.1 1.0
CD2 B:HIS740 3.7 25.9 1.0
N20 B:4482 3.7 18.5 1.0
C4 B:4482 3.7 21.4 1.0
O B:HOH2643 3.8 35.4 1.0
NE2 B:HIS740 3.8 24.7 1.0
OG B:SER630 3.9 25.5 0.7
C12 B:4482 3.9 20.9 1.0
C5 B:4482 4.2 21.6 1.0
CZ B:ARG125 4.3 32.8 1.0
CD B:GLU205 4.5 29.4 1.0
CG B:HIS740 4.7 26.6 1.0
F9 B:4482 4.8 21.9 1.0
CZ B:TYR662 4.8 24.7 1.0
CB B:ASN710 4.9 25.2 1.0
CE1 B:HIS740 4.9 25.9 1.0
OG B:SER630 4.9 25.3 0.3
C15 B:4482 5.0 22.6 1.0

Fluorine binding site 9 out of 12 in 2qoe

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Fluorine binding site 9 out of 12 in the Human Dipeptidyl Peptidase IV in Complex with A Triazolopiperazine- Based Beta Amino Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Human Dipeptidyl Peptidase IV in Complex with A Triazolopiperazine- Based Beta Amino Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2

b:21.1
occ:1.00
 F8 B:4482 0.0 21.1 1.0
C5 B:4482 1.3 21.6 1.0
C4 B:4482 2.4 21.4 1.0
C6 B:4482 2.4 21.8 1.0
F9 B:4482 2.7 21.9 1.0
CD2 B:TYR631 3.4 23.2 1.0
CE1 B:TYR666 3.5 26.9 1.0
OH B:TYR666 3.5 26.2 1.0
C3 B:4482 3.6 21.7 1.0
CZ B:TYR666 3.6 26.3 1.0
CB B:TYR631 3.7 24.6 1.0
C1 B:4482 3.7 20.4 1.0
CG B:TYR631 4.0 23.9 1.0
CA B:TYR631 4.0 24.6 1.0
N B:TYR631 4.0 25.2 1.0
CH2 B:TRP659 4.1 24.7 1.0
C2 B:4482 4.2 21.1 1.0
CD1 B:TYR666 4.4 26.3 1.0
CE2 B:TYR662 4.4 21.3 1.0
CE2 B:TYR631 4.4 23.4 1.0
OH B:TYR547 4.4 26.3 1.0
CG2 B:VAL656 4.4 22.5 1.0
OG B:SER630 4.5 25.5 0.7
CZ3 B:TRP659 4.5 23.5 1.0
CE2 B:TYR666 4.5 26.3 1.0
CZ B:TYR662 4.6 24.7 1.0
OH B:TYR662 4.8 26.9 1.0
CD2 B:TYR662 4.9 22.7 1.0
C B:SER630 4.9 25.7 1.0
C11 B:4482 4.9 20.9 1.0
O B:HOH2538 4.9 30.0 1.0

Fluorine binding site 10 out of 12 in 2qoe

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Fluorine binding site 10 out of 12 in the Human Dipeptidyl Peptidase IV in Complex with A Triazolopiperazine- Based Beta Amino Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Human Dipeptidyl Peptidase IV in Complex with A Triazolopiperazine- Based Beta Amino Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2

b:40.0
occ:1.00
 F29 B:4482 0.0 40.0 1.0
C41 B:4482 1.3 38.2 1.0
F28 B:4482 2.2 41.0 1.0
F27 B:4482 2.2 39.3 1.0
C40 B:4482 2.3 38.0 1.0
N41 B:4482 2.8 35.8 1.0
N39 B:4482 3.5 36.4 1.0
OH B:TYR585 3.9 26.5 1.0
C28 B:4482 4.0 34.9 1.0
N27 B:4482 4.3 35.4 1.0
CE2 B:PHE357 4.9 28.6 1.0

Reference:

J.E.Kowalchick, B.Leiting, K.D.Pryor, F.Marsilio, J.K.Wu, H.He, K.A.Lyons, G.J.Eiermann, A.Petrov, G.Scapin, R.A.Patel, N.A.Thornberry, A.E.Weber, D.Kim. Design, Synthesis, and Biological Evaluation of Triazolopiperazine-Based Beta-Amino Amides As Potent, Orally Active Dipeptidyl Peptidase IV (Dpp-4) Inhibitors. Bioorg.Med.Chem.Lett. V. 17 5934 2007.
ISSN: ISSN 0960-894X
PubMed: 17827003
DOI: 10.1016/J.BMCL.2007.07.100
Page generated: Wed Jul 31 15:51:16 2024

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