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Fluorine in PDB 2iit: Human Dipeptidyl Peptidase 4 in Complex with A Diazepan-2-One Inhibitor

Enzymatic activity of Human Dipeptidyl Peptidase 4 in Complex with A Diazepan-2-One Inhibitor

All present enzymatic activity of Human Dipeptidyl Peptidase 4 in Complex with A Diazepan-2-One Inhibitor:
3.4.14.5;

Protein crystallography data

The structure of Human Dipeptidyl Peptidase 4 in Complex with A Diazepan-2-One Inhibitor, PDB code: 2iit was solved by G.Scapin, T.Biftu, A.E.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 118.224, 125.197, 136.870, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 2iit:

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

Fluorine binding site 1 out of 12 in 2iit

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Fluorine binding site 1 out of 12 in the Human Dipeptidyl Peptidase 4 in Complex with A Diazepan-2-One 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 4 in Complex with A Diazepan-2-One Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F9001

b:28.3
occ:1.00
 F9 A:8729001 0.0 28.3 1.0
C5 A:8729001 1.3 25.6 1.0
C4 A:8729001 2.4 22.6 1.0
C6 A:8729001 2.4 26.3 1.0
F41 A:8729001 2.7 27.3 1.0
CD2 A:TYR631 3.3 20.7 1.0
CB A:TYR631 3.4 20.8 1.0
C3 A:8729001 3.6 23.0 1.0
C1 A:8729001 3.7 24.6 1.0
OH A:TYR666 3.7 22.4 1.0
CA A:TYR631 3.7 19.6 1.0
CG A:TYR631 3.8 20.1 1.0
CE1 A:TYR666 3.8 17.8 1.0
N A:TYR631 3.8 19.4 1.0
CZ A:TYR666 3.9 20.0 1.0
CH2 A:TRP659 4.0 21.1 1.0
C2 A:8729001 4.1 22.1 1.0
CG2 A:VAL656 4.3 14.9 1.0
CE2 A:TYR631 4.3 20.4 1.0
CZ3 A:TRP659 4.3 20.9 1.0
CE2 A:TYR662 4.6 15.7 1.0
OH A:TYR547 4.6 19.7 1.0
CD1 A:TYR666 4.7 16.2 1.0
C A:SER630 4.7 20.9 1.0
CZ A:TYR662 4.8 17.0 1.0
CE2 A:TYR666 4.8 19.0 1.0
C11 A:8729001 4.9 22.2 1.0
CD2 A:TYR662 4.9 15.0 1.0
O A:HOH9209 5.0 28.0 1.0
OH A:TYR662 5.0 14.8 1.0
CB A:SER630 5.0 22.4 1.0

Fluorine binding site 2 out of 12 in 2iit

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Fluorine binding site 2 out of 12 in the Human Dipeptidyl Peptidase 4 in Complex with A Diazepan-2-One 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 4 in Complex with A Diazepan-2-One Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F9001

b:25.1
occ:1.00
 F10 A:8729001 0.0 25.1 1.0
C2 A:8729001 1.3 22.1 1.0
C1 A:8729001 2.4 24.6 1.0
C3 A:8729001 2.4 23.0 1.0
C11 A:8729001 2.9 22.2 1.0
ND2 A:ASN710 3.2 17.7 1.0
NH2 A:ARG125 3.3 29.0 1.0
N20 A:8729001 3.4 19.2 1.0
OD1 A:ASN710 3.5 20.1 1.0
OH A:TYR662 3.5 14.8 1.0
CG A:ASN710 3.6 19.4 1.0
OE2 A:GLU205 3.6 23.4 1.0
C6 A:8729001 3.6 26.3 1.0
C4 A:8729001 3.7 22.6 1.0
O A:HOH9194 3.8 33.4 1.0
NE2 A:HIS740 3.8 20.7 1.0
C12 A:8729001 3.8 24.2 1.0
CD2 A:HIS740 3.9 18.4 1.0
C5 A:8729001 4.1 25.6 1.0
OG A:SER630 4.5 28.7 1.0
CZ A:ARG125 4.6 28.7 1.0
CZ A:TYR662 4.6 17.0 1.0
C15 A:8729001 4.7 24.6 1.0
CD A:GLU205 4.7 23.3 1.0
CE1 A:HIS740 4.7 19.8 1.0
F41 A:8729001 4.7 27.3 1.0
CB A:ASN710 4.8 18.3 1.0
CB A:SER630 4.8 22.4 1.0
CG A:HIS740 4.8 19.0 1.0

Fluorine binding site 3 out of 12 in 2iit

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Fluorine binding site 3 out of 12 in the Human Dipeptidyl Peptidase 4 in Complex with A Diazepan-2-One 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 4 in Complex with A Diazepan-2-One Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F9001

b:27.3
occ:1.00
 F41 A:8729001 0.0 27.3 1.0
C6 A:8729001 1.3 26.3 1.0
C5 A:8729001 2.4 25.6 1.0
C1 A:8729001 2.4 24.6 1.0
F9 A:8729001 2.7 28.3 1.0
CG2 A:VAL656 3.1 14.9 1.0
CG2 A:VAL711 3.2 16.6 1.0
C2 A:8729001 3.7 22.1 1.0
C4 A:8729001 3.7 22.6 1.0
N A:TYR631 3.7 19.4 1.0
C A:SER630 3.7 20.9 1.0
CA A:SER630 3.8 21.8 1.0
CB A:SER630 3.9 22.4 1.0
CB A:VAL656 4.2 17.8 1.0
C3 A:8729001 4.2 23.0 1.0
CE1 A:TYR662 4.2 16.9 1.0
O A:SER630 4.2 21.6 1.0
CA A:TYR631 4.3 19.6 1.0
CZ A:TYR662 4.4 17.0 1.0
N A:VAL656 4.6 19.0 1.0
CD1 A:TYR662 4.6 17.1 1.0
OH A:TYR662 4.6 14.8 1.0
CB A:VAL711 4.6 18.2 1.0
F10 A:8729001 4.7 25.1 1.0
CE1 A:HIS740 4.8 19.8 1.0
O A:ALA654 4.8 19.9 1.0
OG A:SER630 4.8 28.7 1.0
CA A:VAL656 4.8 18.5 1.0
NE2 A:HIS740 4.8 20.7 1.0
CE2 A:TYR662 4.9 15.7 1.0
CB A:TYR631 4.9 20.8 1.0
CG1 A:VAL711 4.9 14.4 1.0

Fluorine binding site 4 out of 12 in 2iit

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Fluorine binding site 4 out of 12 in the Human Dipeptidyl Peptidase 4 in Complex with A Diazepan-2-One 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 4 in Complex with A Diazepan-2-One Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F9001

b:40.8
occ:1.00
 F45 A:8729001 0.0 40.8 1.0
C42 A:8729001 1.3 38.0 1.0
F46 A:8729001 2.1 39.5 1.0
F47 A:8729001 2.1 38.1 1.0
C37 A:8729001 2.3 35.2 1.0
O A:HOH9254 2.9 29.6 1.0
C30 A:8729001 3.8 33.2 1.0
O A:HOH9364 4.0 24.1 1.0
O A:HOH9365 4.2 24.5 1.0
OH A:TYR547 4.6 19.7 1.0
O22 A:8729001 4.7 25.4 1.0
O39 A:8729001 4.7 36.1 1.0
C29 A:8729001 4.8 32.9 1.0
N19 A:8729001 4.8 29.0 1.0
CZ A:TYR547 4.9 16.8 1.0
C16 A:8729001 4.9 27.8 1.0

Fluorine binding site 5 out of 12 in 2iit

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Fluorine binding site 5 out of 12 in the Human Dipeptidyl Peptidase 4 in Complex with A Diazepan-2-One 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 4 in Complex with A Diazepan-2-One Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F9001

b:39.5
occ:1.00
 F46 A:8729001 0.0 39.5 1.0
C42 A:8729001 1.3 38.0 1.0
F45 A:8729001 2.1 40.8 1.0
F47 A:8729001 2.1 38.1 1.0
C37 A:8729001 2.4 35.2 1.0
O22 A:8729001 3.0 25.4 1.0
C30 A:8729001 3.1 33.2 1.0
O A:HOH9365 3.1 24.5 1.0
O A:HOH9209 3.3 28.0 1.0
O A:HOH9364 3.4 24.1 1.0
C16 A:8729001 3.7 27.8 1.0
OH A:TYR547 3.9 19.7 1.0
C29 A:8729001 3.9 32.9 1.0
N19 A:8729001 3.9 29.0 1.0
O A:HOH9254 4.0 29.6 1.0
O39 A:8729001 4.0 36.1 1.0
O A:HOH9262 4.1 29.1 1.0
CE1 A:TYR547 4.3 15.5 1.0
CZ A:TYR547 4.4 16.8 1.0
CZ A:PHE357 4.4 21.3 1.0
CE1 A:PHE357 4.6 19.4 1.0
C11 A:8729001 4.7 22.2 1.0
N28 A:8729001 4.8 31.8 1.0
C15 A:8729001 5.0 24.6 1.0

Fluorine binding site 6 out of 12 in 2iit

Go back to Fluorine Binding Sites List in 2iit
Fluorine binding site 6 out of 12 in the Human Dipeptidyl Peptidase 4 in Complex with A Diazepan-2-One 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 4 in Complex with A Diazepan-2-One Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F9001

b:38.1
occ:1.00
 F47 A:8729001 0.0 38.1 1.0
C42 A:8729001 1.3 38.0 1.0
F46 A:8729001 2.1 39.5 1.0
F45 A:8729001 2.1 40.8 1.0
C37 A:8729001 2.4 35.2 1.0
O22 A:8729001 3.0 25.4 1.0
C30 A:8729001 3.1 33.2 1.0
C16 A:8729001 3.1 27.8 1.0
N19 A:8729001 3.4 29.0 1.0
C11 A:8729001 3.4 22.2 1.0
C15 A:8729001 3.8 24.6 1.0
OH A:TYR547 4.0 19.7 1.0
O A:HOH9209 4.2 28.0 1.0
C12 A:8729001 4.3 24.2 1.0
O A:HOH9254 4.5 29.6 1.0
C29 A:8729001 4.5 32.9 1.0
O A:HOH9194 4.5 33.4 1.0
C3 A:8729001 4.6 23.0 1.0
NH2 A:ARG125 4.7 29.0 1.0
C25 A:8729001 4.7 29.2 1.0
CZ A:TYR547 4.9 16.8 1.0
O39 A:8729001 5.0 36.1 1.0

Fluorine binding site 7 out of 12 in 2iit

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Fluorine binding site 7 out of 12 in the Human Dipeptidyl Peptidase 4 in Complex with A Diazepan-2-One 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 4 in Complex with A Diazepan-2-One Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F9002

b:27.9
occ:1.00
 F9 B:8729002 0.0 27.9 1.0
C5 B:8729002 1.3 25.9 1.0
C4 B:8729002 2.3 26.0 1.0
C6 B:8729002 2.4 26.7 1.0
F41 B:8729002 2.7 31.1 1.0
CD2 B:TYR631 3.4 20.7 1.0
CB B:TYR631 3.6 21.7 1.0
OH B:TYR666 3.6 23.8 1.0
C3 B:8729002 3.6 24.7 1.0
C1 B:8729002 3.7 26.6 1.0
CE1 B:TYR666 3.7 22.0 1.0
CZ B:TYR666 3.8 22.8 1.0
CA B:TYR631 3.9 21.0 1.0
CG B:TYR631 4.0 21.7 1.0
N B:TYR631 4.0 21.2 1.0
CH2 B:TRP659 4.1 22.8 1.0
C2 B:8729002 4.1 25.3 1.0
CG2 B:VAL656 4.3 20.3 1.0
CE2 B:TYR662 4.3 18.2 1.0
CZ3 B:TRP659 4.4 21.2 1.0
CE2 B:TYR631 4.5 21.8 1.0
CD1 B:TYR666 4.5 21.5 1.0
OH B:TYR547 4.5 21.6 1.0
CZ B:TYR662 4.5 20.7 1.0
CE2 B:TYR666 4.6 21.5 1.0
OH B:TYR662 4.7 20.2 1.0
CD2 B:TYR662 4.8 16.9 1.0
C11 B:8729002 4.8 24.4 1.0
C B:SER630 4.8 22.6 1.0
O B:HOH9578 4.9 31.0 1.0

Fluorine binding site 8 out of 12 in 2iit

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Fluorine binding site 8 out of 12 in the Human Dipeptidyl Peptidase 4 in Complex with A Diazepan-2-One 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 4 in Complex with A Diazepan-2-One Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F9002

b:23.8
occ:1.00
 F10 B:8729002 0.0 23.8 1.0
C2 B:8729002 1.3 25.3 1.0
C1 B:8729002 2.4 26.6 1.0
C3 B:8729002 2.4 24.7 1.0
C11 B:8729002 2.9 24.4 1.0
NH2 B:ARG125 3.2 25.5 1.0
ND2 B:ASN710 3.2 18.1 1.0
OD1 B:ASN710 3.4 21.3 1.0
OE2 B:GLU205 3.4 23.7 1.0
OH B:TYR662 3.5 20.2 1.0
CG B:ASN710 3.5 20.5 1.0
N20 B:8729002 3.5 22.1 1.0
C6 B:8729002 3.7 26.7 1.0
CD2 B:HIS740 3.7 17.6 1.0
C4 B:8729002 3.7 26.0 1.0
NE2 B:HIS740 3.7 20.0 1.0
C12 B:8729002 3.9 25.1 1.0
C5 B:8729002 4.1 25.9 1.0
CZ B:ARG125 4.5 27.3 1.0
OG B:SER630 4.6 25.3 1.0
CD B:GLU205 4.6 24.0 1.0
CB B:ASN710 4.7 19.8 1.0
CZ B:TYR662 4.7 20.7 1.0
C15 B:8729002 4.7 26.1 1.0
CG B:HIS740 4.7 20.4 1.0
F41 B:8729002 4.7 31.1 1.0
CE1 B:HIS740 4.8 19.4 1.0
CB B:SER630 5.0 22.5 1.0

Fluorine binding site 9 out of 12 in 2iit

Go back to Fluorine Binding Sites List in 2iit
Fluorine binding site 9 out of 12 in the Human Dipeptidyl Peptidase 4 in Complex with A Diazepan-2-One 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 4 in Complex with A Diazepan-2-One Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F9002

b:31.1
occ:1.00
 F41 B:8729002 0.0 31.1 1.0
C6 B:8729002 1.3 26.7 1.0
C5 B:8729002 2.3 25.9 1.0
C1 B:8729002 2.4 26.6 1.0
F9 B:8729002 2.7 27.9 1.0
CG2 B:VAL656 3.0 20.3 1.0
CG2 B:VAL711 3.2 19.2 1.0
C4 B:8729002 3.6 26.0 1.0
C2 B:8729002 3.6 25.3 1.0
N B:TYR631 3.7 21.2 1.0
C B:SER630 3.8 22.6 1.0
CA B:SER630 4.0 23.8 1.0
CB B:SER630 4.0 22.5 1.0
CE1 B:TYR662 4.1 19.3 1.0
CZ B:TYR662 4.1 20.7 1.0
C3 B:8729002 4.2 24.7 1.0
CB B:VAL656 4.3 21.5 1.0
OH B:TYR662 4.4 20.2 1.0
CA B:TYR631 4.4 21.0 1.0
O B:SER630 4.4 22.6 1.0
CD1 B:TYR662 4.6 18.8 1.0
CE2 B:TYR662 4.6 18.2 1.0
CB B:VAL711 4.7 20.0 1.0
NE2 B:HIS740 4.7 20.0 1.0
CE1 B:HIS740 4.7 19.4 1.0
F10 B:8729002 4.7 23.8 1.0
N B:VAL656 4.8 22.1 1.0
OG B:SER630 4.8 25.3 1.0
CB B:TYR631 4.9 21.7 1.0
CA B:VAL656 5.0 21.2 1.0

Fluorine binding site 10 out of 12 in 2iit

Go back to Fluorine Binding Sites List in 2iit
Fluorine binding site 10 out of 12 in the Human Dipeptidyl Peptidase 4 in Complex with A Diazepan-2-One 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 4 in Complex with A Diazepan-2-One Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F9002

b:46.9
occ:1.00
 F45 B:8729002 0.0 46.9 1.0
C42 B:8729002 1.3 43.3 1.0
F46 B:8729002 2.1 44.9 1.0
F47 B:8729002 2.1 44.4 1.0
C37 B:8729002 2.3 40.3 1.0
O B:HOH9673 2.7 38.9 1.0
C30 B:8729002 3.7 35.1 1.0
O B:HOH9692 4.2 34.2 1.0
O B:HOH9698 4.4 34.3 1.0
O39 B:8729002 4.4 37.9 1.0
C29 B:8729002 4.6 35.4 1.0
O22 B:8729002 4.7 26.3 1.0
OH B:TYR547 4.8 21.6 1.0
N19 B:8729002 4.8 31.4 1.0
C16 B:8729002 4.9 28.4 1.0
O B:HOH9602 5.0 37.4 1.0

Reference:

T.Biftu, D.Feng, X.Qian, G.B.Liang, G.Kieczykowski, G.Eiermann, H.He, B.Leiting, K.Lyons, A.Petrov, R.Sinha-Roy, B.Zhang, G.Scapin, S.Patel, Y.D.Gao, S.Singh, J.Wu, X.Zhang, N.A.Thornberry, A.E.Weber. (3R)-4-[(3R)-3-Amino-4-(2,4,5-Trifluorophenyl) Butanoyl]-3-(2,2,2-Trifluoroethyl)-1,4-Diazepan-2-One, A Selective Dipeptidyl Peptidase IV Inhibitor For the Treatment of Type 2 Diabetes Bioorg.Med.Chem.Lett. V. 17 49 2007.
ISSN: ISSN 0960-894X
PubMed: 17055272
DOI: 10.1016/J.BMCL.2006.09.099
Page generated: Mon Jul 14 13:28:59 2025

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