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Fluorine in PDB 2p8s: Human Dipeptidyl Peptidase IV/CD26 in Complex with A Cyclohexalamine Inhibitor

Enzymatic activity of Human Dipeptidyl Peptidase IV/CD26 in Complex with A Cyclohexalamine Inhibitor

All present enzymatic activity of Human Dipeptidyl Peptidase IV/CD26 in Complex with A Cyclohexalamine Inhibitor:
3.4.14.5;

Protein crystallography data

The structure of Human Dipeptidyl Peptidase IV/CD26 in Complex with A Cyclohexalamine Inhibitor, PDB code: 2p8s was solved by G.Scapin, T.Biftu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 118.139, 126.174, 137.340, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 2p8s:

The structure of Human Dipeptidyl Peptidase IV/CD26 in Complex with A Cyclohexalamine Inhibitor also contains other interesting chemical elements:

Sodium (Na) 1 atom

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Fluorine atom in the Human Dipeptidyl Peptidase IV/CD26 in Complex with A Cyclohexalamine Inhibitor (pdb code 2p8s). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 24 binding sites of Fluorine where determined in the Human Dipeptidyl Peptidase IV/CD26 in Complex with A Cyclohexalamine Inhibitor, PDB code: 2p8s:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 24 in 2p8s

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Fluorine binding site 1 out of 24 in the Human Dipeptidyl Peptidase IV/CD26 in Complex with A Cyclohexalamine 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/CD26 in Complex with A Cyclohexalamine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:22.4
occ:0.55
F36 A:4171001 0.0 22.4 0.6
F36 A:4171001 0.4 23.3 0.5
C5 A:4171001 1.3 20.5 0.6
C5 A:4171001 1.6 22.6 0.5
C4 A:4171001 2.4 18.9 0.6
C6 A:4171001 2.4 19.7 0.6
C4 A:4171001 2.4 22.0 0.5
C6 A:4171001 2.8 22.0 0.5
F43 A:4171001 2.8 20.7 0.6
OH A:TYR666 3.1 20.7 1.0
F43 A:4171001 3.2 22.2 0.5
CZ A:TYR666 3.2 18.8 1.0
CD2 A:TYR631 3.2 15.1 1.0
CE1 A:TYR666 3.3 18.4 1.0
C1 A:4171001 3.7 18.9 0.6
C3 A:4171001 3.7 18.7 0.6
CB A:TYR631 3.7 15.5 1.0
C3 A:4171001 3.8 22.3 0.5
CG A:TYR631 3.9 16.4 1.0
C1 A:4171001 4.0 21.6 0.5
CH2 A:TRP659 4.0 14.7 1.0
CE2 A:TYR666 4.1 19.6 1.0
C2 A:4171001 4.1 18.0 0.6
CD1 A:TYR666 4.2 17.7 1.0
CA A:TYR631 4.2 15.7 1.0
CZ3 A:TRP659 4.3 15.4 1.0
CE2 A:TYR631 4.3 15.9 1.0
O A:HOH9114 4.3 20.7 1.0
CE2 A:TYR662 4.4 14.4 1.0
C2 A:4171001 4.4 21.7 0.5
N A:TYR631 4.5 17.1 1.0
OH A:TYR547 4.5 25.6 1.0
CG2 A:VAL656 4.7 13.0 1.0
CZ A:TYR662 4.7 15.5 1.0
CD2 A:TYR662 4.8 14.6 1.0
CD2 A:TYR666 4.8 18.4 1.0
CG A:TYR666 4.9 18.4 1.0
OH A:TYR662 4.9 14.7 1.0
C9 A:4171001 5.0 17.3 0.6
OG A:SER630 5.0 22.3 1.0

Fluorine binding site 2 out of 24 in 2p8s

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Fluorine binding site 2 out of 24 in the Human Dipeptidyl Peptidase IV/CD26 in Complex with A Cyclohexalamine 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/CD26 in Complex with A Cyclohexalamine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:23.3
occ:0.45
F36 A:4171001 0.0 23.3 0.5
F36 A:4171001 0.4 22.4 0.6
C5 A:4171001 1.1 20.5 0.6
C5 A:4171001 1.3 22.6 0.5
C6 A:4171001 2.0 19.7 0.6
C4 A:4171001 2.3 18.9 0.6
C4 A:4171001 2.4 22.0 0.5
C6 A:4171001 2.4 22.0 0.5
F43 A:4171001 2.4 20.7 0.6
F43 A:4171001 2.8 22.2 0.5
C1 A:4171001 3.3 18.9 0.6
CD2 A:TYR631 3.4 15.1 1.0
OH A:TYR666 3.5 20.7 1.0
C3 A:4171001 3.5 18.7 0.6
CB A:TYR631 3.6 15.5 1.0
CZ A:TYR666 3.6 18.8 1.0
C1 A:4171001 3.7 21.6 0.5
C3 A:4171001 3.7 22.3 0.5
CE1 A:TYR666 3.7 18.4 1.0
C2 A:4171001 3.9 18.0 0.6
CG A:TYR631 3.9 16.4 1.0
CA A:TYR631 4.0 15.7 1.0
C2 A:4171001 4.1 21.7 0.5
N A:TYR631 4.1 17.1 1.0
CH2 A:TRP659 4.2 14.7 1.0
OH A:TYR547 4.4 25.6 1.0
CE2 A:TYR666 4.4 19.6 1.0
CE2 A:TYR662 4.4 14.4 1.0
O A:HOH9114 4.4 20.7 1.0
CZ3 A:TRP659 4.4 15.4 1.0
CE2 A:TYR631 4.5 15.9 1.0
CG2 A:VAL656 4.5 13.0 1.0
CD1 A:TYR666 4.6 17.7 1.0
OG A:SER630 4.6 22.3 1.0
CZ A:TYR662 4.7 15.5 1.0
OH A:TYR662 4.8 14.7 1.0
CD2 A:TYR662 4.9 14.6 1.0
C9 A:4171001 4.9 17.3 0.6
C9 A:4171001 5.0 22.2 0.5

Fluorine binding site 3 out of 24 in 2p8s

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Fluorine binding site 3 out of 24 in the Human Dipeptidyl Peptidase IV/CD26 in Complex with A Cyclohexalamine 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/CD26 in Complex with A Cyclohexalamine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:19.1
occ:0.55
F37 A:4171001 0.0 19.1 0.6
F37 A:4171001 0.4 22.6 0.5
C2 A:4171001 1.1 21.7 0.5
C2 A:4171001 1.3 18.0 0.6
C1 A:4171001 2.0 21.6 0.5
C3 A:4171001 2.3 22.3 0.5
C1 A:4171001 2.3 18.9 0.6
C3 A:4171001 2.4 18.7 0.6
C9 A:4171001 2.8 17.3 0.6
C9 A:4171001 3.0 22.2 0.5
ND2 A:ASN710 3.1 16.5 1.0
C6 A:4171001 3.3 22.0 0.5
NH2 A:ARG125 3.3 18.9 1.0
C4 A:4171001 3.5 22.0 0.5
OH A:TYR662 3.5 14.7 1.0
CG A:ASN710 3.6 17.0 1.0
OE2 A:GLU205 3.6 18.7 1.0
OD1 A:ASN710 3.6 17.8 1.0
N38 A:4171001 3.6 16.3 0.6
C6 A:4171001 3.6 19.7 0.6
O A:HOH9105 3.6 24.1 1.0
O A:HOH9037 3.6 22.5 1.0
C4 A:4171001 3.7 18.9 0.6
NE2 A:HIS740 3.7 18.9 1.0
CD2 A:HIS740 3.7 19.0 1.0
N38 A:4171001 3.7 22.4 0.5
C14 A:4171001 3.8 17.4 0.6
OG A:SER630 3.8 22.3 1.0
C5 A:4171001 3.9 22.6 0.5
C14 A:4171001 4.0 22.7 0.5
C10 A:4171001 4.0 18.1 0.6
C5 A:4171001 4.1 20.5 0.6
C10 A:4171001 4.2 23.1 0.5
F43 A:4171001 4.3 22.2 0.5
CZ A:TYR662 4.6 15.5 1.0
CZ A:ARG125 4.6 20.2 1.0
F43 A:4171001 4.7 20.7 0.6
CB A:ASN710 4.7 16.2 1.0
CE1 A:HIS740 4.7 18.7 1.0
CD A:GLU205 4.7 19.8 1.0
O A:HOH9384 4.8 45.4 1.0
CG A:HIS740 4.8 20.5 1.0
C13 A:4171001 4.8 17.7 0.6
C11 A:4171001 5.0 17.8 0.6

Fluorine binding site 4 out of 24 in 2p8s

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Fluorine binding site 4 out of 24 in the Human Dipeptidyl Peptidase IV/CD26 in Complex with A Cyclohexalamine 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/CD26 in Complex with A Cyclohexalamine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:22.6
occ:0.45
F37 A:4171001 0.0 22.6 0.5
F37 A:4171001 0.4 19.1 0.6
C2 A:4171001 1.3 21.7 0.5
C2 A:4171001 1.6 18.0 0.6
C1 A:4171001 2.3 21.6 0.5
C3 A:4171001 2.4 22.3 0.5
C3 A:4171001 2.5 18.7 0.6
C1 A:4171001 2.7 18.9 0.6
C9 A:4171001 2.7 17.3 0.6
C9 A:4171001 2.9 22.2 0.5
NH2 A:ARG125 3.0 18.9 1.0
ND2 A:ASN710 3.0 16.5 1.0
OE2 A:GLU205 3.3 18.7 1.0
N38 A:4171001 3.5 16.3 0.6
O A:HOH9105 3.5 24.1 1.0
CG A:ASN710 3.6 17.0 1.0
N38 A:4171001 3.6 22.4 0.5
C6 A:4171001 3.6 22.0 0.5
OH A:TYR662 3.6 14.7 1.0
OD1 A:ASN710 3.7 17.8 1.0
C4 A:4171001 3.7 22.0 0.5
C14 A:4171001 3.7 17.4 0.6
O A:HOH9037 3.7 22.5 1.0
C4 A:4171001 3.8 18.9 0.6
CD2 A:HIS740 3.8 19.0 1.0
C14 A:4171001 3.9 22.7 0.5
NE2 A:HIS740 3.9 18.9 1.0
C6 A:4171001 3.9 19.7 0.6
C10 A:4171001 3.9 18.1 0.6
C10 A:4171001 4.1 23.1 0.5
OG A:SER630 4.1 22.3 1.0
C5 A:4171001 4.1 22.6 0.5
CZ A:ARG125 4.3 20.2 1.0
C5 A:4171001 4.4 20.5 0.6
CD A:GLU205 4.5 19.8 1.0
C13 A:4171001 4.6 17.7 0.6
O A:HOH9384 4.7 45.4 1.0
F43 A:4171001 4.7 22.2 0.5
CB A:ASN710 4.7 16.2 1.0
C11 A:4171001 4.8 17.8 0.6
CZ A:TYR662 4.8 15.5 1.0
CG A:HIS740 4.9 20.5 1.0
C13 A:4171001 4.9 23.5 0.5
CE1 A:HIS740 4.9 18.7 1.0

Fluorine binding site 5 out of 24 in 2p8s

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Fluorine binding site 5 out of 24 in the Human Dipeptidyl Peptidase IV/CD26 in Complex with A Cyclohexalamine 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/CD26 in Complex with A Cyclohexalamine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:31.3
occ:0.55
F40 A:4171001 0.0 31.3 0.6
C39 A:4171001 1.3 29.6 0.6
F42 A:4171001 2.2 30.6 0.6
F41 A:4171001 2.2 30.4 0.6
C33 A:4171001 2.3 26.8 0.5
N34 A:4171001 2.8 26.7 0.6
F41 A:4171001 2.8 34.4 0.5
F40 A:4171001 3.2 35.8 0.5
C39 A:4171001 3.4 33.2 0.5
N24 A:4171001 3.6 24.8 0.6
C33 A:4171001 3.8 32.3 0.6
N35 A:4171001 4.0 25.0 0.6
N34 A:4171001 4.1 31.7 0.5
CB A:SER209 4.2 20.7 1.0
OG A:SER209 4.3 24.3 1.0
C25 A:4171001 4.4 24.1 0.6
C23 A:4171001 4.5 24.8 0.6
N24 A:4171001 4.6 31.0 0.5
F42 A:4171001 4.7 33.1 0.5
N35 A:4171001 4.9 31.1 0.5

Fluorine binding site 6 out of 24 in 2p8s

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Fluorine binding site 6 out of 24 in the Human Dipeptidyl Peptidase IV/CD26 in Complex with A Cyclohexalamine 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/CD26 in Complex with A Cyclohexalamine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:35.8
occ:0.45
F40 A:4171001 0.0 35.8 0.5
C39 A:4171001 1.3 33.2 0.5
F41 A:4171001 1.8 30.4 0.6
F42 A:4171001 2.2 33.1 0.5
F41 A:4171001 2.2 34.4 0.5
C33 A:4171001 2.3 32.3 0.6
C39 A:4171001 2.6 29.6 0.6
F42 A:4171001 2.6 30.6 0.6
N34 A:4171001 2.8 31.7 0.5
F40 A:4171001 3.2 31.3 0.6
N24 A:4171001 3.6 31.0 0.5
C33 A:4171001 3.9 26.8 0.5
N35 A:4171001 4.0 31.1 0.5
C23 A:4171001 4.2 24.8 0.6
O A:HOH9119 4.3 24.9 1.0
NH1 A:ARG358 4.4 41.8 1.0
N24 A:4171001 4.4 24.8 0.6
C25 A:4171001 4.4 30.4 0.5
C23 A:4171001 4.5 29.4 0.5
CZ A:ARG358 4.6 40.3 1.0
NH2 A:ARG358 4.9 39.3 1.0

Fluorine binding site 7 out of 24 in 2p8s

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Fluorine binding site 7 out of 24 in the Human Dipeptidyl Peptidase IV/CD26 in Complex with A Cyclohexalamine 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/CD26 in Complex with A Cyclohexalamine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:30.4
occ:0.55
F41 A:4171001 0.0 30.4 0.6
F41 A:4171001 0.9 34.4 0.5
C39 A:4171001 1.3 33.2 0.5
C39 A:4171001 1.3 29.6 0.6
F40 A:4171001 1.8 35.8 0.5
C33 A:4171001 2.0 32.3 0.6
F42 A:4171001 2.2 30.6 0.6
F40 A:4171001 2.2 31.3 0.6
C33 A:4171001 2.3 26.8 0.5
F42 A:4171001 2.5 33.1 0.5
N34 A:4171001 2.8 31.7 0.5
N24 A:4171001 2.9 31.0 0.5
N24 A:4171001 3.0 24.8 0.6
C23 A:4171001 3.3 24.8 0.6
N34 A:4171001 3.4 26.7 0.6
OG A:SER209 3.5 24.3 1.0
C23 A:4171001 3.5 29.4 0.5
N35 A:4171001 3.8 31.1 0.5
C25 A:4171001 3.8 30.4 0.5
CB A:SER209 4.0 20.7 1.0
NH1 A:ARG358 4.0 41.8 1.0
C25 A:4171001 4.1 24.1 0.6
N35 A:4171001 4.3 25.0 0.6
CZ A:ARG358 4.8 40.3 1.0
C22 A:4171001 4.8 23.8 0.6

Fluorine binding site 8 out of 24 in 2p8s

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Fluorine binding site 8 out of 24 in the Human Dipeptidyl Peptidase IV/CD26 in Complex with A Cyclohexalamine 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/CD26 in Complex with A Cyclohexalamine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:34.4
occ:0.45
F41 A:4171001 0.0 34.4 0.5
F41 A:4171001 0.9 30.4 0.6
C39 A:4171001 1.3 33.2 0.5
C39 A:4171001 2.1 29.6 0.6
F40 A:4171001 2.2 35.8 0.5
F42 A:4171001 2.2 33.1 0.5
C33 A:4171001 2.3 32.3 0.6
C33 A:4171001 2.7 26.8 0.5
F40 A:4171001 2.8 31.3 0.6
OG A:SER209 2.9 24.3 1.0
N24 A:4171001 3.0 31.0 0.5
F42 A:4171001 3.0 30.6 0.6
N24 A:4171001 3.2 24.8 0.6
NH1 A:ARG358 3.3 41.8 1.0
C23 A:4171001 3.3 29.4 0.5
N34 A:4171001 3.4 31.7 0.5
CB A:SER209 3.5 20.7 1.0
C23 A:4171001 3.5 24.8 0.6
N34 A:4171001 3.7 26.7 0.6
CZ A:ARG358 4.1 40.3 1.0
C25 A:4171001 4.1 30.4 0.5
C25 A:4171001 4.3 24.1 0.6
N35 A:4171001 4.3 31.1 0.5
N35 A:4171001 4.5 25.0 0.6
NH2 A:ARG358 4.6 39.3 1.0
C22 A:4171001 4.8 28.9 0.5
O A:HOH9502 4.9 49.3 1.0
CA A:SER209 4.9 21.1 1.0
C22 A:4171001 5.0 23.8 0.6
NE A:ARG358 5.0 37.4 1.0

Fluorine binding site 9 out of 24 in 2p8s

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Fluorine binding site 9 out of 24 in the Human Dipeptidyl Peptidase IV/CD26 in Complex with A Cyclohexalamine 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/CD26 in Complex with A Cyclohexalamine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:30.6
occ:0.55
F42 A:4171001 0.0 30.6 0.6
C39 A:4171001 1.3 29.6 0.6
N34 A:4171001 2.1 31.7 0.5
F41 A:4171001 2.2 30.4 0.6
F40 A:4171001 2.2 31.3 0.6
C33 A:4171001 2.3 26.8 0.5
C33 A:4171001 2.5 32.3 0.6
F40 A:4171001 2.6 35.8 0.5
C39 A:4171001 2.8 33.2 0.5
N35 A:4171001 2.9 31.1 0.5
N24 A:4171001 3.0 24.8 0.6
F41 A:4171001 3.0 34.4 0.5
C23 A:4171001 3.3 24.8 0.6
N34 A:4171001 3.4 26.7 0.6
N24 A:4171001 3.4 31.0 0.5
C25 A:4171001 3.6 30.4 0.5
F42 A:4171001 4.1 33.1 0.5
C25 A:4171001 4.1 24.1 0.6
N35 A:4171001 4.3 25.0 0.6
C23 A:4171001 4.6 29.4 0.5
C22 A:4171001 4.7 23.8 0.6
O A:HOH9501 4.9 44.4 1.0
C26 A:4171001 5.0 29.4 0.6

Fluorine binding site 10 out of 24 in 2p8s

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Fluorine binding site 10 out of 24 in the Human Dipeptidyl Peptidase IV/CD26 in Complex with A Cyclohexalamine 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/CD26 in Complex with A Cyclohexalamine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:33.1
occ:0.45
F42 A:4171001 0.0 33.1 0.5
C39 A:4171001 1.3 33.2 0.5
F40 A:4171001 2.2 35.8 0.5
F41 A:4171001 2.2 34.4 0.5
C33 A:4171001 2.3 32.3 0.6
F41 A:4171001 2.5 30.4 0.6
N24 A:4171001 3.0 31.0 0.5
NH1 A:ARG358 3.2 41.8 1.0
C23 A:4171001 3.3 29.4 0.5
O A:HOH9119 3.3 24.9 1.0
N34 A:4171001 3.4 31.7 0.5
CZ A:ARG358 3.7 40.3 1.0
C39 A:4171001 3.8 29.6 0.6
O A:HOH9502 3.9 49.3 1.0
CD A:ARG358 3.9 34.4 1.0
C23 A:4171001 3.9 24.8 0.6
NE A:ARG358 4.0 37.4 1.0
C25 A:4171001 4.1 30.4 0.5
F42 A:4171001 4.1 30.6 0.6
CB A:PHE357 4.2 20.2 1.0
N35 A:4171001 4.3 31.1 0.5
OG A:SER209 4.4 24.3 1.0
C33 A:4171001 4.4 26.8 0.5
N24 A:4171001 4.4 24.8 0.6
CG A:ARG358 4.5 29.9 1.0
NH2 A:ARG358 4.5 39.3 1.0
F40 A:4171001 4.7 31.3 0.6
C22 A:4171001 4.7 28.9 0.5
CD2 A:PHE357 4.8 21.7 1.0
CG A:PHE357 4.9 20.6 1.0

Reference:

T.Biftu, G.Scapin, S.Singh, D.Feng, J.W.Becker, G.Eiermann, H.He, K.Lyons, S.Patel, A.Petrov, R.Sinha-Roy, B.Zhang, J.Wu, X.Zhang, G.A.Doss, N.A.Thornberry, A.E.Weber. Rational Design of A Novel, Potent, and Orally Bioavailable Cyclohexylamine Dpp-4 Inhibitor By Application of Molecular Modeling and X-Ray Crystallography of Sitagliptin Bioorg.Med.Chem.Lett. V. 17 3384 2007.
ISSN: ISSN 0960-894X
PubMed: 17433672
DOI: 10.1016/J.BMCL.2007.03.095
Page generated: Sun Dec 13 11:38:50 2020

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