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Fluorine in PDB 5y7h: Crystal Structure of Human DPP4 in Complex with INHIBITOR3

Enzymatic activity of Crystal Structure of Human DPP4 in Complex with INHIBITOR3

All present enzymatic activity of Crystal Structure of Human DPP4 in Complex with INHIBITOR3:
3.4.14.5;

Protein crystallography data

The structure of Crystal Structure of Human DPP4 in Complex with INHIBITOR3, PDB code: 5y7h was solved by H.K.Lee, E.E.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.17 / 3.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 64.301, 126.420, 113.382, 90.00, 100.43, 90.00
R / Rfree (%) 19.9 / 24.5

Fluorine Binding Sites:

Pages:

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

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of Human DPP4 in Complex with INHIBITOR3 (pdb code 5y7h). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Crystal Structure of Human DPP4 in Complex with INHIBITOR3, PDB code: 5y7h:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 5y7h

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Fluorine binding site 1 out of 12 in the Crystal Structure of Human DPP4 in Complex with INHIBITOR3


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 DPP4 in Complex with INHIBITOR3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:36.7
occ:1.00
 F20 A:8O3801 0.0 36.7 1.0
C06 A:8O3801 1.4 35.0 1.0
C01 A:8O3801 2.4 33.0 1.0
C05 A:8O3801 2.4 38.1 1.0
H051 A:8O3801 2.6 45.8 1.0
F21 A:8O3801 2.7 32.6 1.0
CD2 A:TYR631 3.3 28.5 1.0
CE1 A:TYR666 3.6 28.4 1.0
C02 A:8O3801 3.6 34.3 1.0
C04 A:8O3801 3.6 35.0 1.0
CB A:TYR631 3.7 24.4 1.0
OH A:TYR666 3.8 33.1 1.0
CZ A:TYR666 3.8 32.3 1.0
CG A:TYR631 4.0 26.2 1.0
CA A:TYR631 4.1 27.9 1.0
C03 A:8O3801 4.1 31.3 1.0
N A:TYR631 4.2 28.8 1.0
CD1 A:TYR666 4.3 30.2 1.0
CE2 A:TYR662 4.3 28.4 1.0
CH2 A:TRP659 4.3 25.7 1.0
OG A:SER630 4.4 28.9 1.0
CE2 A:TYR631 4.4 30.4 1.0
H021 A:8O3801 4.4 41.1 1.0
CG2 A:VAL656 4.4 22.4 1.0
CZ A:TYR662 4.4 28.4 1.0
CZ3 A:TRP659 4.5 26.1 1.0
OH A:TYR662 4.6 30.8 1.0
H4 A:8O3801 4.6 40.7 1.0
CE2 A:TYR666 4.7 33.4 1.0
OH A:TYR547 4.7 35.0 1.0
H1 A:8O3801 4.8 41.6 1.0
CD2 A:TYR662 4.8 29.4 1.0
C07 A:8O3801 4.9 39.4 1.0
CE1 A:TYR662 5.0 30.7 1.0

Fluorine binding site 2 out of 12 in 5y7h

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Fluorine binding site 2 out of 12 in the Crystal Structure of Human DPP4 in Complex with INHIBITOR3


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 DPP4 in Complex with INHIBITOR3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:32.6
occ:1.00
 F21 A:8O3801 0.0 32.6 1.0
C01 A:8O3801 1.4 33.0 1.0
C06 A:8O3801 2.4 35.0 1.0
C02 A:8O3801 2.4 34.3 1.0
H021 A:8O3801 2.6 41.1 1.0
F20 A:8O3801 2.7 36.7 1.0
CG2 A:VAL711 3.0 22.3 1.0
CG2 A:VAL656 3.2 22.4 1.0
OG A:SER630 3.3 28.9 1.0
C05 A:8O3801 3.6 38.1 1.0
C03 A:8O3801 3.6 31.3 1.0
N A:TYR631 3.7 28.8 1.0
C A:SER630 3.9 24.9 1.0
CE1 A:TYR662 4.1 30.7 1.0
C04 A:8O3801 4.1 35.0 1.0
CA A:SER630 4.2 24.3 1.0
CZ A:TYR662 4.3 28.4 1.0
CB A:SER630 4.3 24.9 1.0
CA A:TYR631 4.4 27.9 1.0
H051 A:8O3801 4.4 45.8 1.0
CB A:VAL711 4.4 26.5 1.0
OH A:TYR662 4.4 30.8 1.0
O A:SER630 4.5 27.2 1.0
NE2 A:HIS740 4.5 25.2 1.0
CE1 A:HIS740 4.5 25.8 1.0
CD1 A:TYR662 4.6 31.1 1.0
CB A:VAL656 4.7 21.0 1.0
F22 A:8O3801 4.8 34.9 1.0
CG1 A:VAL711 4.8 25.4 1.0
CB A:TYR631 4.8 24.4 1.0
CE2 A:TYR662 4.9 28.4 1.0
O A:ALA654 5.0 22.0 1.0

Fluorine binding site 3 out of 12 in 5y7h

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Fluorine binding site 3 out of 12 in the Crystal Structure of Human DPP4 in Complex with INHIBITOR3


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 DPP4 in Complex with INHIBITOR3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:34.9
occ:1.00
 F22 A:8O3801 0.0 34.9 1.0
C03 A:8O3801 1.4 31.3 1.0
C02 A:8O3801 2.4 34.3 1.0
C04 A:8O3801 2.4 35.0 1.0
H071 A:8O3801 2.4 47.2 1.0
H021 A:8O3801 2.5 41.1 1.0
NH2 A:ARG125 2.6 30.2 1.0
C07 A:8O3801 2.9 39.4 1.0
ND2 A:ASN710 3.1 33.5 1.0
H3 A:8O3801 3.4 40.7 1.0
OE1 A:GLU205 3.5 27.9 1.0
H072 A:8O3801 3.5 47.2 1.0
C01 A:8O3801 3.6 33.0 1.0
C05 A:8O3801 3.6 38.1 1.0
CG A:ASN710 3.6 27.9 1.0
H4 A:8O3801 3.7 40.7 1.0
CD2 A:HIS740 3.8 24.6 1.0
OD1 A:ASN710 3.8 28.6 1.0
NE2 A:HIS740 3.8 25.2 1.0
OH A:TYR662 3.9 30.8 1.0
N19 A:8O3801 3.9 33.9 1.0
CZ A:ARG125 3.9 21.8 1.0
C08 A:8O3801 4.0 34.6 1.0
OG A:SER630 4.0 28.9 1.0
C06 A:8O3801 4.1 35.0 1.0
H051 A:8O3801 4.4 45.8 1.0
H091 A:8O3801 4.6 41.8 1.0
H1 A:8O3801 4.6 41.6 1.0
CD A:GLU205 4.6 31.1 1.0
NH1 A:ARG125 4.7 21.1 1.0
F21 A:8O3801 4.8 32.6 1.0
CB A:ASN710 4.8 25.3 1.0
NE A:ARG125 4.8 26.2 1.0
CG A:HIS740 4.8 22.5 1.0
CE1 A:HIS740 4.9 25.8 1.0
C09 A:8O3801 4.9 34.8 1.0
CB A:SER630 4.9 24.9 1.0
O12 A:8O3802 5.0 63.8 1.0

Fluorine binding site 4 out of 12 in 5y7h

Go back to Fluorine Binding Sites List in 5y7h
Fluorine binding site 4 out of 12 in the Crystal Structure of Human DPP4 in Complex with INHIBITOR3


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 DPP4 in Complex with INHIBITOR3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F802

b:55.4
occ:1.00
 F20 A:8O3802 0.0 55.4 1.0
C06 A:8O3802 1.4 53.5 1.0
C01 A:8O3802 2.4 55.7 1.0
C05 A:8O3802 2.4 47.8 1.0
H051 A:8O3802 2.6 57.4 1.0
H131 A:8O3801 2.7 42.3 1.0
F21 A:8O3802 2.8 67.3 1.0
NE2 A:HIS126 3.2 30.2 1.0
CE1 A:HIS126 3.5 31.9 1.0
OG A:SER209 3.5 35.3 1.0
CD A:ARG125 3.5 26.4 1.0
C02 A:8O3802 3.6 55.5 1.0
C04 A:8O3802 3.7 62.3 1.0
C13 A:8O3801 3.7 35.3 1.0
NE A:ARG125 3.9 26.2 1.0
H4 A:8O3802 4.0 56.2 1.0
CB A:SER209 4.0 31.5 1.0
H132 A:8O3801 4.1 42.3 1.0
C03 A:8O3802 4.1 68.1 1.0
C14 A:8O3801 4.2 52.1 1.0
H091 A:8O3801 4.2 41.8 1.0
H161 A:8O3801 4.4 59.8 1.0
H021 A:8O3802 4.4 66.6 1.0
CZ A:ARG125 4.4 21.8 1.0
CD2 A:HIS126 4.5 28.0 1.0
NH1 A:ARG125 4.5 21.1 1.0
N11 A:8O3801 4.5 40.8 1.0
O18 A:8O3801 4.5 63.9 1.0
O A:GLU205 4.6 27.9 1.0
H1 A:8O3802 4.7 57.8 1.0
ND1 A:HIS126 4.8 28.8 1.0
N15 A:8O3801 4.8 48.6 1.0
CA A:SER209 4.8 32.2 1.0
N19 A:8O3802 4.8 46.9 1.0
CG A:ARG125 4.9 29.0 1.0
C07 A:8O3802 4.9 67.7 1.0
C16 A:8O3801 5.0 49.8 1.0

Fluorine binding site 5 out of 12 in 5y7h

Go back to Fluorine Binding Sites List in 5y7h
Fluorine binding site 5 out of 12 in the Crystal Structure of Human DPP4 in Complex with INHIBITOR3


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 DPP4 in Complex with INHIBITOR3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F802

b:67.3
occ:1.00
 F21 A:8O3802 0.0 67.3 1.0
C01 A:8O3802 1.4 55.7 1.0
C02 A:8O3802 2.4 55.5 1.0
C06 A:8O3802 2.4 53.5 1.0
H021 A:8O3802 2.6 66.6 1.0
F20 A:8O3802 2.8 55.4 1.0
OG A:SER209 2.8 35.3 1.0
CB A:SER209 3.0 31.5 1.0
C03 A:8O3802 3.6 68.1 1.0
C05 A:8O3802 3.6 47.8 1.0
C14 A:8O3801 3.8 52.1 1.0
O18 A:8O3801 3.8 63.9 1.0
H131 A:8O3801 3.8 42.3 1.0
N15 A:8O3801 4.0 48.6 1.0
H2 A:8O3801 4.1 58.4 1.0
C04 A:8O3802 4.1 62.3 1.0
CE1 A:HIS126 4.1 31.9 1.0
H161 A:8O3801 4.2 59.8 1.0
NE2 A:HIS126 4.3 30.2 1.0
C13 A:8O3801 4.3 35.3 1.0
H051 A:8O3802 4.4 57.4 1.0
CA A:SER209 4.5 32.2 1.0
C16 A:8O3801 4.7 49.8 1.0
F22 A:8O3802 4.8 76.7 1.0
O A:SER209 4.9 32.5 1.0
H132 A:8O3801 4.9 42.3 1.0

Fluorine binding site 6 out of 12 in 5y7h

Go back to Fluorine Binding Sites List in 5y7h
Fluorine binding site 6 out of 12 in the Crystal Structure of Human DPP4 in Complex with INHIBITOR3


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 DPP4 in Complex with INHIBITOR3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F802

b:76.7
occ:1.00
 F22 A:8O3802 0.0 76.7 1.0
C03 A:8O3802 1.4 68.1 1.0
C02 A:8O3802 2.4 55.5 1.0
C04 A:8O3802 2.4 62.3 1.0
H071 A:8O3802 2.5 81.2 1.0
H021 A:8O3802 2.6 66.6 1.0
C07 A:8O3802 2.9 67.7 1.0
H072 A:8O3802 3.2 81.2 1.0
H161 A:8O3801 3.2 59.8 1.0
C01 A:8O3802 3.6 55.7 1.0
C05 A:8O3802 3.7 47.8 1.0
H162 A:8O3801 3.9 59.8 1.0
C16 A:8O3801 4.0 49.8 1.0
H3 A:8O3802 4.1 56.2 1.0
C06 A:8O3802 4.1 53.5 1.0
C08 A:8O3802 4.2 48.2 1.0
H051 A:8O3802 4.4 57.4 1.0
N19 A:8O3802 4.5 46.9 1.0
H4 A:8O3802 4.5 56.2 1.0
N15 A:8O3801 4.7 48.6 1.0
H091 A:8O3802 4.7 45.0 1.0
H2 A:8O3801 4.8 58.4 1.0
F21 A:8O3802 4.8 67.3 1.0
H1 A:8O3802 4.8 57.8 1.0

Fluorine binding site 7 out of 12 in 5y7h

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Fluorine binding site 7 out of 12 in the Crystal Structure of Human DPP4 in Complex with INHIBITOR3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of Human DPP4 in Complex with INHIBITOR3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:63.6
occ:1.00
 F20 B:8O3801 0.0 63.6 1.0
C06 B:8O3801 1.4 60.6 1.0
C05 B:8O3801 2.4 58.5 1.0
C01 B:8O3801 2.4 54.3 1.0
H051 B:8O3801 2.6 70.2 1.0
F21 B:8O3801 2.8 41.2 1.0
H161 B:8O3802 3.5 64.3 1.0
C02 B:8O3801 3.6 49.5 1.0
C04 B:8O3801 3.7 60.2 1.0
H162 B:8O3802 3.8 64.3 1.0
H2 B:8O3802 3.9 59.2 1.0
C16 B:8O3802 4.0 53.6 1.0
C03 B:8O3801 4.1 50.3 1.0
N15 B:8O3802 4.2 49.3 1.0
H021 B:8O3801 4.4 59.4 1.0
H071 B:8O3801 4.8 75.0 1.0
C07 B:8O3801 4.9 62.5 1.0

Fluorine binding site 8 out of 12 in 5y7h

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Fluorine binding site 8 out of 12 in the Crystal Structure of Human DPP4 in Complex with INHIBITOR3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of Human DPP4 in Complex with INHIBITOR3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:41.2
occ:1.00
 F21 B:8O3801 0.0 41.2 1.0
C01 B:8O3801 1.4 54.3 1.0
C06 B:8O3801 2.4 60.6 1.0
C02 B:8O3801 2.4 49.5 1.0
H021 B:8O3801 2.6 59.4 1.0
F20 B:8O3801 2.8 63.6 1.0
H2 B:8O3802 3.3 59.2 1.0
N15 B:8O3802 3.3 49.3 1.0
H161 B:8O3802 3.4 64.3 1.0
C05 B:8O3801 3.6 58.5 1.0
C03 B:8O3801 3.7 50.3 1.0
C14 B:8O3802 3.7 51.1 1.0
C16 B:8O3802 3.9 53.6 1.0
O18 B:8O3802 3.9 52.7 1.0
OG B:SER209 4.1 31.8 1.0
H131 B:8O3802 4.1 42.4 1.0
C04 B:8O3801 4.1 60.2 1.0
H162 B:8O3802 4.3 64.3 1.0
CB B:SER209 4.3 29.3 1.0
H051 B:8O3801 4.4 70.2 1.0
C13 B:8O3802 4.5 35.3 1.0
O B:HOH917 4.7 36.9 1.0
F22 B:8O3801 4.8 47.2 1.0
O B:HOH902 4.8 35.0 1.0

Fluorine binding site 9 out of 12 in 5y7h

Go back to Fluorine Binding Sites List in 5y7h
Fluorine binding site 9 out of 12 in the Crystal Structure of Human DPP4 in Complex with INHIBITOR3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of Human DPP4 in Complex with INHIBITOR3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:47.2
occ:1.00
 F22 B:8O3801 0.0 47.2 1.0
C03 B:8O3801 1.4 50.3 1.0
H4 B:8O3801 2.1 67.1 1.0
C02 B:8O3801 2.4 49.5 1.0
C04 B:8O3801 2.4 60.2 1.0
H021 B:8O3801 2.5 59.4 1.0
H1 B:8O3801 2.6 67.8 1.0
N19 B:8O3801 2.8 55.9 1.0
C08 B:8O3801 2.9 56.5 1.0
C07 B:8O3801 2.9 62.5 1.0
NH1 B:ARG125 3.0 41.9 1.0
H072 B:8O3801 3.1 75.0 1.0
H3 B:8O3801 3.3 67.1 1.0
CZ B:ARG125 3.5 30.6 1.0
H131 B:8O3802 3.6 42.4 1.0
C01 B:8O3801 3.6 54.3 1.0
C05 B:8O3801 3.7 58.5 1.0
H161 B:8O3802 3.8 64.3 1.0
H071 B:8O3801 3.8 75.0 1.0
NH2 B:ARG125 3.9 22.0 1.0
NE B:ARG125 4.1 31.5 1.0
C06 B:8O3801 4.1 60.6 1.0
H091 B:8O3802 4.2 46.4 1.0
N11 B:8O3802 4.3 34.4 1.0
C13 B:8O3802 4.4 35.3 1.0
H071 B:8O3802 4.4 40.4 1.0
H051 B:8O3801 4.4 70.2 1.0
C09 B:8O3801 4.4 46.4 1.0
CD B:ARG125 4.4 28.6 1.0
C10 B:8O3802 4.5 35.2 1.0
H171 B:8O3802 4.6 59.6 1.0
C16 B:8O3802 4.6 53.6 1.0
O B:HOH902 4.6 35.0 1.0
H072 B:8O3802 4.7 40.4 1.0
C17 B:8O3802 4.7 49.6 1.0
H092 B:8O3801 4.7 55.7 1.0
F21 B:8O3801 4.8 41.2 1.0
C09 B:8O3802 4.8 38.7 1.0
H091 B:8O3801 4.9 55.7 1.0
O12 B:8O3802 5.0 39.8 1.0

Fluorine binding site 10 out of 12 in 5y7h

Go back to Fluorine Binding Sites List in 5y7h
Fluorine binding site 10 out of 12 in the Crystal Structure of Human DPP4 in Complex with INHIBITOR3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of Human DPP4 in Complex with INHIBITOR3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F802

b:31.3
occ:1.00
 F20 B:8O3802 0.0 31.3 1.0
C06 B:8O3802 1.4 31.4 1.0
C01 B:8O3802 2.4 37.0 1.0
C05 B:8O3802 2.4 30.4 1.0
H051 B:8O3802 2.6 36.4 1.0
F21 B:8O3802 2.8 38.7 1.0
CD2 B:TYR631 3.4 24.1 1.0
CE1 B:TYR666 3.4 25.4 1.0
OH B:TYR666 3.6 33.8 1.0
CZ B:TYR666 3.6 28.4 1.0
C02 B:8O3802 3.6 35.6 1.0
C04 B:8O3802 3.7 30.5 1.0
CB B:TYR631 3.9 27.4 1.0
CH2 B:TRP659 4.1 27.5 1.0
CG B:TYR631 4.1 21.9 1.0
C03 B:8O3802 4.1 30.3 1.0
CZ3 B:TRP659 4.2 24.9 1.0
CD1 B:TYR666 4.2 27.1 1.0
CE2 B:TYR631 4.3 27.7 1.0
CZ B:TYR662 4.3 34.2 1.0
CE2 B:TYR662 4.3 36.3 1.0
H021 B:8O3802 4.4 42.8 1.0
CA B:TYR631 4.4 26.9 1.0
CG2 B:VAL656 4.4 27.2 1.0
OG B:SER630 4.4 27.8 1.0
N B:TYR631 4.5 24.9 1.0
OH B:TYR662 4.5 30.4 1.0
CE2 B:TYR666 4.5 27.9 1.0
H4 B:8O3802 4.6 45.5 1.0
H1 B:8O3802 4.7 42.7 1.0
CE1 B:TYR662 4.8 34.5 1.0
CD2 B:TYR662 4.8 31.8 1.0
OH B:TYR547 4.8 33.6 1.0
C07 B:8O3802 4.9 33.7 1.0

Reference:

H.K.Lee, M.K.Kim, H.D.Kim, H.J.Kim, J.W.Kim, J.O.Lee, C.W.Kim, E.E.Kim. Unique Binding Mode of Evogliptin with Human Dipeptidyl Peptidase IV. Biochem.Biophys.Res.Commun. V. 494 452 2017.
ISSN: ESSN 1090-2104
PubMed: 29061303
DOI: 10.1016/J.BBRC.2017.10.101
Page generated: Thu Aug 1 17:10:12 2024

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