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Fluorine in PDB 1x70: Human Dipeptidyl Peptidase IV in Complex with A Beta Amino Acid Inhibitor

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

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

Protein crystallography data

The structure of Human Dipeptidyl Peptidase IV in Complex with A Beta Amino Acid Inhibitor, PDB code: 1x70 was solved by D.Kim, L.Wang, M.Beconi, G.J.Eiermann, M.H.Fisher, H.He, G.J.Hickey, B.Leiting, K.Lyons, 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 (°) 118.253, 125.680, 137.206, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 1x70:

The structure of Human Dipeptidyl Peptidase IV in Complex with A 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 Beta Amino Acid Inhibitor (pdb code 1x70). 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 Beta Amino Acid Inhibitor, PDB code: 1x70:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 1x70

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Fluorine binding site 1 out of 12 in the Human Dipeptidyl Peptidase IV in Complex with A 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 Beta Amino Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:26.5
occ:1.00
 F9 A:715801 0.0 26.5 1.0
C5 A:715801 1.3 25.5 1.0
C6 A:715801 2.4 25.5 1.0
C4 A:715801 2.4 22.9 1.0
F46 A:715801 2.7 28.5 1.0
CD2 A:TYR631 3.3 15.3 1.0
CB A:TYR631 3.6 15.2 1.0
CE1 A:TYR666 3.7 17.4 1.0
C3 A:715801 3.7 23.2 1.0
C1 A:715801 3.7 23.9 1.0
OH A:TYR666 3.7 20.3 1.0
CZ A:TYR666 3.8 18.6 1.0
CA A:TYR631 3.9 15.8 1.0
CG A:TYR631 3.9 16.3 1.0
N A:TYR631 4.0 16.0 1.0
CH2 A:TRP659 4.0 16.0 1.0
C2 A:715801 4.1 22.9 1.0
CG2 A:VAL656 4.3 16.0 1.0
CZ3 A:TRP659 4.3 17.0 1.0
CE2 A:TYR631 4.4 16.7 1.0
CE2 A:TYR662 4.4 14.6 1.0
CD1 A:TYR666 4.5 17.6 1.0
CZ A:TYR662 4.6 13.9 1.0
OH A:TYR547 4.7 22.0 1.0
CE2 A:TYR666 4.7 17.7 1.0
CD2 A:TYR662 4.8 13.7 1.0
OH A:TYR662 4.8 15.6 1.0
C A:SER630 4.9 17.6 1.0
C11 A:715801 4.9 20.7 1.0

Fluorine binding site 2 out of 12 in 1x70

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Fluorine binding site 2 out of 12 in the Human Dipeptidyl Peptidase IV in Complex with A 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 Beta Amino Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:22.9
occ:1.00
 F10 A:715801 0.0 22.9 1.0
C2 A:715801 1.3 22.9 1.0
C1 A:715801 2.4 23.9 1.0
C3 A:715801 2.4 23.2 1.0
C11 A:715801 2.8 20.7 1.0
ND2 A:ASN710 3.2 18.6 1.0
NH2 A:ARG125 3.2 23.2 1.0
OE2 A:GLU205 3.5 20.6 1.0
N20 A:715801 3.6 19.5 1.0
OD1 A:ASN710 3.6 20.2 1.0
OH A:TYR662 3.6 15.6 1.0
CG A:ASN710 3.6 19.5 1.0
O A:HOH1927 3.6 39.0 1.0
C6 A:715801 3.6 25.5 1.0
C4 A:715801 3.7 22.9 1.0
C12 A:715801 3.8 21.4 1.0
NE2 A:HIS740 3.9 21.7 1.0
CD2 A:HIS740 3.9 21.1 1.0
C5 A:715801 4.1 25.5 1.0
CZ A:ARG125 4.5 23.4 1.0
CD A:GLU205 4.6 20.9 1.0
C15 A:715801 4.7 22.0 1.0
F46 A:715801 4.7 28.5 1.0
OG A:SER630 4.7 26.2 1.0
CZ A:TYR662 4.7 13.9 1.0
CE1 A:HIS740 4.8 21.9 1.0
CB A:ASN710 4.8 16.9 1.0
CB A:SER630 4.8 18.5 1.0
CG A:HIS740 4.9 21.6 1.0

Fluorine binding site 3 out of 12 in 1x70

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Fluorine binding site 3 out of 12 in the Human Dipeptidyl Peptidase IV in Complex with A 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 Beta Amino Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:38.7
occ:1.00
 F43 A:715801 0.0 38.7 1.0
C42 A:715801 1.3 36.1 1.0
F45 A:715801 2.2 37.2 1.0
F44 A:715801 2.2 39.1 1.0
C39 A:715801 2.3 34.2 1.0
N40 A:715801 2.7 32.9 1.0
NE A:ARG358 3.0 35.0 1.0
O A:HOH1986 3.2 38.5 1.0
CG A:ARG358 3.5 29.4 1.0
N27 A:715801 3.6 31.1 1.0
CD A:ARG358 3.6 31.6 1.0
O A:HOH1639 3.7 21.4 1.0
CZ A:ARG358 3.9 37.6 1.0
N41 A:715801 3.9 31.9 1.0
NH2 A:ARG358 4.0 37.7 1.0
O A:VAL207 4.2 22.2 1.0
CB A:PHE357 4.3 23.2 1.0
C28 A:715801 4.4 30.6 1.0
C26 A:715801 4.5 30.8 1.0
CB A:ARG358 4.7 26.0 1.0
O A:HOH1605 4.7 33.7 1.0
N A:ARG358 4.9 24.4 1.0

Fluorine binding site 4 out of 12 in 1x70

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Fluorine binding site 4 out of 12 in the Human Dipeptidyl Peptidase IV in Complex with A 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 Beta Amino Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:39.1
occ:1.00
 F44 A:715801 0.0 39.1 1.0
C42 A:715801 1.3 36.1 1.0
F43 A:715801 2.2 38.7 1.0
F45 A:715801 2.2 37.2 1.0
C39 A:715801 2.3 34.2 1.0
N27 A:715801 3.0 31.1 1.0
OG A:SER209 3.1 25.8 1.0
O A:VAL207 3.2 22.2 1.0
C26 A:715801 3.3 30.8 1.0
N40 A:715801 3.4 32.9 1.0
CB A:SER209 3.6 23.6 1.0
O A:HOH1605 3.7 33.7 1.0
NE A:ARG358 3.9 35.0 1.0
C A:VAL207 4.1 22.0 1.0
C28 A:715801 4.1 30.6 1.0
N A:SER209 4.2 22.2 1.0
C A:PHE208 4.3 23.1 1.0
N41 A:715801 4.3 31.9 1.0
CZ A:ARG358 4.4 37.6 1.0
NH2 A:ARG358 4.5 37.7 1.0
C25 A:715801 4.5 28.2 1.0
O A:GLU206 4.5 21.2 1.0
CD A:ARG358 4.5 31.6 1.0
CA A:SER209 4.5 21.9 1.0
O A:PHE208 4.5 23.0 1.0
N A:PHE208 4.7 21.7 1.0
CA A:PHE208 4.7 23.2 1.0
CG A:ARG358 4.9 29.4 1.0
CA A:VAL207 4.9 20.6 1.0
C A:GLU206 4.9 20.3 1.0

Fluorine binding site 5 out of 12 in 1x70

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Fluorine binding site 5 out of 12 in the Human Dipeptidyl Peptidase IV in Complex with A 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 Beta Amino Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:37.2
occ:1.00
 F45 A:715801 0.0 37.2 1.0
C42 A:715801 1.3 36.1 1.0
F43 A:715801 2.2 38.7 1.0
F44 A:715801 2.2 39.1 1.0
C39 A:715801 2.3 34.2 1.0
N27 A:715801 3.0 31.1 1.0
C26 A:715801 3.3 30.8 1.0
N40 A:715801 3.4 32.9 1.0
O A:VAL207 3.4 22.2 1.0
CB A:PHE357 3.5 23.2 1.0
O A:GLU206 3.5 21.2 1.0
CG A:ARG358 3.5 29.4 1.0
CD A:ARG358 3.7 31.6 1.0
NE A:ARG358 3.8 35.0 1.0
CB A:ARG358 4.0 26.0 1.0
C28 A:715801 4.2 30.6 1.0
C A:PHE357 4.2 24.0 1.0
C A:VAL207 4.3 22.0 1.0
N41 A:715801 4.3 31.9 1.0
N A:ARG358 4.4 24.4 1.0
C A:GLU206 4.4 20.3 1.0
O A:HOH1551 4.4 22.7 1.0
CA A:PHE357 4.5 23.5 1.0
O A:PHE357 4.5 26.0 1.0
CG A:PHE357 4.5 22.1 1.0
CA A:VAL207 4.5 20.6 1.0
O A:HOH1639 4.6 21.4 1.0
O A:HOH1986 4.7 38.5 1.0
CZ A:ARG358 4.8 37.6 1.0
C25 A:715801 4.8 28.2 1.0
CA A:ARG358 4.9 24.9 1.0
N A:VAL207 4.9 20.1 1.0
OG A:SER209 5.0 25.8 1.0

Fluorine binding site 6 out of 12 in 1x70

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Fluorine binding site 6 out of 12 in the Human Dipeptidyl Peptidase IV in Complex with A 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 Beta Amino Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:28.5
occ:1.00
 F46 A:715801 0.0 28.5 1.0
C6 A:715801 1.3 25.5 1.0
C1 A:715801 2.3 23.9 1.0
C5 A:715801 2.4 25.5 1.0
F9 A:715801 2.7 26.5 1.0
CG2 A:VAL656 3.1 16.0 1.0
CG2 A:VAL711 3.2 12.7 1.0
C2 A:715801 3.6 22.9 1.0
C4 A:715801 3.7 22.9 1.0
N A:TYR631 3.7 16.0 1.0
C A:SER630 3.9 17.6 1.0
CB A:SER630 3.9 18.5 1.0
CA A:SER630 4.0 18.0 1.0
CE1 A:TYR662 4.1 14.9 1.0
C3 A:715801 4.2 23.2 1.0
CZ A:TYR662 4.2 13.9 1.0
CB A:VAL656 4.3 17.5 1.0
CA A:TYR631 4.4 15.8 1.0
OH A:TYR662 4.4 15.6 1.0
O A:SER630 4.4 18.9 1.0
CD1 A:TYR662 4.5 13.8 1.0
CB A:VAL711 4.6 15.6 1.0
F10 A:715801 4.7 22.9 1.0
CE2 A:TYR662 4.7 14.6 1.0
N A:VAL656 4.7 16.9 1.0
CG1 A:VAL711 4.8 14.2 1.0
CE1 A:HIS740 4.8 21.9 1.0
NE2 A:HIS740 4.9 21.7 1.0
OG A:SER630 4.9 26.2 1.0
CB A:TYR631 4.9 15.2 1.0
CA A:VAL656 5.0 17.6 1.0
O A:ALA654 5.0 15.6 1.0
CG A:TYR662 5.0 14.6 1.0

Fluorine binding site 7 out of 12 in 1x70

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Fluorine binding site 7 out of 12 in the Human Dipeptidyl Peptidase IV in Complex with A 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 Beta Amino Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:26.7
occ:1.00
 F9 B:715801 0.0 26.7 1.0
C5 B:715801 1.3 24.7 1.0
C4 B:715801 2.3 23.7 1.0
C6 B:715801 2.4 24.6 1.0
F46 B:715801 2.7 27.2 1.0
CD2 B:TYR631 3.3 21.1 1.0
CE1 B:TYR666 3.6 18.7 1.0
OH B:TYR666 3.6 21.1 1.0
C3 B:715801 3.7 23.3 1.0
C1 B:715801 3.7 24.8 1.0
CB B:TYR631 3.7 19.1 1.0
CZ B:TYR666 3.7 20.4 1.0
CG B:TYR631 4.0 19.5 1.0
CH2 B:TRP659 4.0 17.5 1.0
CA B:TYR631 4.1 18.9 1.0
C2 B:715801 4.1 24.1 1.0
N B:TYR631 4.2 20.0 1.0
CZ3 B:TRP659 4.3 16.6 1.0
CE2 B:TYR662 4.4 15.1 1.0
CG2 B:VAL656 4.4 16.3 1.0
CE2 B:TYR631 4.4 21.0 1.0
CD1 B:TYR666 4.4 18.1 1.0
OG B:SER630 4.5 28.5 1.0
CE2 B:TYR666 4.5 18.8 1.0
CZ B:TYR662 4.6 16.4 1.0
OH B:TYR547 4.6 20.7 1.0
CD2 B:TYR662 4.8 15.6 1.0
OH B:TYR662 4.8 18.2 1.0
C11 B:715801 4.9 21.3 1.0

Fluorine binding site 8 out of 12 in 1x70

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Fluorine binding site 8 out of 12 in the Human Dipeptidyl Peptidase IV in Complex with A 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 Beta Amino Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:26.4
occ:1.00
 F10 B:715801 0.0 26.4 1.0
C2 B:715801 1.3 24.1 1.0
C1 B:715801 2.4 24.8 1.0
C3 B:715801 2.4 23.3 1.0
C11 B:715801 2.8 21.3 1.0
ND2 B:ASN710 3.1 21.2 1.0
NH2 B:ARG125 3.2 25.1 1.0
OE2 B:GLU205 3.5 21.3 1.0
CG B:ASN710 3.6 19.7 1.0
OD1 B:ASN710 3.6 20.3 1.0
OH B:TYR662 3.6 18.2 1.0
N20 B:715801 3.6 18.2 1.0
C6 B:715801 3.7 24.6 1.0
O B:HOH2777 3.7 44.7 1.0
C4 B:715801 3.7 23.7 1.0
NE2 B:HIS740 3.7 21.1 1.0
CD2 B:HIS740 3.7 20.1 1.0
O B:HOH2706 3.8 39.2 1.0
C12 B:715801 3.8 22.1 1.0
OG B:SER630 4.0 28.5 1.0
C5 B:715801 4.2 24.7 1.0
CZ B:ARG125 4.5 26.4 1.0
CD B:GLU205 4.6 22.5 1.0
F46 B:715801 4.7 27.2 1.0
C15 B:715801 4.7 23.6 1.0
CE1 B:HIS740 4.7 20.6 1.0
CG B:HIS740 4.8 20.0 1.0
CB B:ASN710 4.8 18.9 1.0
CZ B:TYR662 4.8 16.4 1.0

Fluorine binding site 9 out of 12 in 1x70

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Fluorine binding site 9 out of 12 in the Human Dipeptidyl Peptidase IV in Complex with A 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 Beta Amino Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:40.0
occ:1.00
 F43 B:715801 0.0 40.0 1.0
C42 B:715801 1.3 38.2 1.0
F44 B:715801 2.2 40.3 1.0
F45 B:715801 2.2 39.5 1.0
C39 B:715801 2.3 36.9 1.0
N40 B:715801 2.7 36.1 1.0
NE B:ARG358 2.8 39.3 1.0
NH2 B:ARG358 3.5 40.7 1.0
CZ B:ARG358 3.6 40.7 1.0
N27 B:715801 3.6 33.5 1.0
CG B:ARG358 3.6 32.4 1.0
CD B:ARG358 3.8 35.5 1.0
O B:HOH2779 3.9 46.8 1.0
N41 B:715801 3.9 35.9 1.0
O B:HOH2492 3.9 25.4 1.0
C28 B:715801 4.4 34.0 1.0
O B:HOH2605 4.4 34.0 1.0
CB B:PHE357 4.5 21.5 1.0
O B:VAL207 4.5 22.4 1.0
C26 B:715801 4.5 32.5 1.0
OG B:SER209 4.8 23.3 1.0
NH1 B:ARG358 4.9 42.1 1.0
CB B:ARG358 4.9 28.4 1.0

Fluorine binding site 10 out of 12 in 1x70

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Fluorine binding site 10 out of 12 in the Human Dipeptidyl Peptidase IV in Complex with A 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 Beta Amino Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:40.3
occ:1.00
 F44 B:715801 0.0 40.3 1.0
C42 B:715801 1.3 38.2 1.0
F43 B:715801 2.2 40.0 1.0
F45 B:715801 2.2 39.5 1.0
C39 B:715801 2.3 36.9 1.0
OG B:SER209 2.9 23.3 1.0
N27 B:715801 3.0 33.5 1.0
C26 B:715801 3.3 32.5 1.0
N40 B:715801 3.4 36.1 1.0
O B:HOH2605 3.4 34.0 1.0
CB B:SER209 3.5 22.1 1.0
O B:VAL207 3.5 22.4 1.0
NE B:ARG358 3.7 39.3 1.0
NH2 B:ARG358 3.8 40.7 1.0
CZ B:ARG358 4.1 40.7 1.0
C28 B:715801 4.1 34.0 1.0
N B:SER209 4.2 22.7 1.0
C B:PHE208 4.2 23.4 1.0
C B:VAL207 4.2 22.3 1.0
N41 B:715801 4.3 35.9 1.0
O B:PHE208 4.4 23.3 1.0
CA B:SER209 4.4 22.0 1.0
C25 B:715801 4.5 29.9 1.0
O B:GLU206 4.6 21.8 1.0
CD B:ARG358 4.6 35.5 1.0
CA B:PHE208 4.8 23.6 1.0
N B:PHE208 4.8 22.7 1.0
CG B:ARG358 4.9 32.4 1.0

Reference:

D.Kim, L.Wang, M.Beconi, G.J.Eiermann, M.H.Fisher, H.He, G.J.Hickey, J.E.Kowalchick, B.Leiting, K.Lyons, F.Marsilio, M.E.Mccann, R.A.Patel, A.Petrov, G.Scapin, S.B.Patel, R.S.Roy, J.K.Wu, M.J.Wyvratt, B.B.Zhang, L.Zhu, N.A.Thornberry, A.E.Weber. (2R)-4-Oxo-4-[3-(Trifluoromethyl)-5,6-Dihydro[1,2, 4]Triazolo[4,3-A]Pyrazin- 7(8H)-Yl]-1-(2,4,5-Trifluorophenyl)Butan-2-Amine: A Potent, Orally Active Dipeptidyl Peptidase IV Inhibitor For the Treatment of Type 2 Diabetes J.Med.Chem. V. 48 141 2005.
ISSN: ISSN 0022-2623
PubMed: 15634008
DOI: 10.1021/JM0493156
Page generated: Wed Jul 31 13:16:15 2024

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