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Fluorine in PDB 2iiv: 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: 2iiv was solved by G.Scapin, A.E.Weber, T.Biftu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 118.192, 125.777, 136.902, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Human Dipeptidyl Peptidase 4 in Complex with A Diazepan-2-One Inhibitor (pdb code 2iiv). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Human Dipeptidyl Peptidase 4 in Complex with A Diazepan-2-One Inhibitor, PDB code: 2iiv:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 2iiv

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Fluorine binding site 1 out of 6 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:25.5
occ:1.00
 F9 A:5659001 0.0 25.5 1.0
C5 A:5659001 1.3 23.7 1.0
C4 A:5659001 2.4 21.4 1.0
C6 A:5659001 2.4 24.3 1.0
F44 A:5659001 2.8 26.7 1.0
CD2 A:TYR631 3.2 17.2 1.0
OH A:TYR666 3.5 20.8 1.0
CB A:TYR631 3.5 17.6 1.0
CE1 A:TYR666 3.6 18.5 1.0
CZ A:TYR666 3.6 20.5 1.0
C3 A:5659001 3.7 20.3 1.0
C1 A:5659001 3.7 22.8 1.0
CG A:TYR631 3.8 17.5 1.0
CA A:TYR631 3.9 16.8 1.0
N A:TYR631 4.1 17.3 1.0
CH2 A:TRP659 4.1 14.7 1.0
C2 A:5659001 4.2 20.6 1.0
CE2 A:TYR631 4.3 17.9 1.0
CZ3 A:TRP659 4.4 16.1 1.0
CD1 A:TYR666 4.4 18.6 1.0
CE2 A:TYR662 4.4 14.9 1.0
OH A:TYR547 4.4 20.6 1.0
CG2 A:VAL656 4.6 12.6 1.0
CE2 A:TYR666 4.6 19.9 1.0
OG A:SER630 4.6 23.2 1.0
CZ A:TYR662 4.7 15.8 1.0
CD2 A:TYR662 4.9 14.8 1.0
OH A:TYR662 4.9 14.6 1.0
C A:SER630 4.9 16.5 1.0
C11 A:5659001 5.0 18.7 1.0

Fluorine binding site 2 out of 6 in 2iiv

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Fluorine binding site 2 out of 6 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:20.7
occ:1.00
 F10 A:5659001 0.0 20.7 1.0
C2 A:5659001 1.3 20.6 1.0
C1 A:5659001 2.4 22.8 1.0
C3 A:5659001 2.4 20.3 1.0
C11 A:5659001 2.8 18.7 1.0
NH2 A:ARG125 3.0 16.8 1.0
ND2 A:ASN710 3.1 16.2 1.0
N20 A:5659001 3.4 17.3 1.0
OE2 A:GLU205 3.4 18.2 1.0
O A:HOH9244 3.6 30.5 1.0
OH A:TYR662 3.6 14.6 1.0
CG A:ASN710 3.7 17.0 1.0
C6 A:5659001 3.7 24.3 1.0
C12 A:5659001 3.7 18.8 1.0
C4 A:5659001 3.8 21.4 1.0
CD2 A:HIS740 3.8 18.7 1.0
NE2 A:HIS740 3.8 19.3 1.0
OD1 A:ASN710 3.8 19.9 1.0
OG A:SER630 3.9 23.2 1.0
C5 A:5659001 4.2 23.7 1.0
CZ A:ARG125 4.4 18.9 1.0
C15 A:5659001 4.5 19.7 1.0
CD A:GLU205 4.5 19.0 1.0
F44 A:5659001 4.7 26.7 1.0
CZ A:TYR662 4.8 15.8 1.0
CB A:ASN710 4.8 16.8 1.0
CE1 A:HIS740 4.8 17.9 1.0
CG A:HIS740 4.9 18.9 1.0

Fluorine binding site 3 out of 6 in 2iiv

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Fluorine binding site 3 out of 6 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:26.7
occ:1.00
 F44 A:5659001 0.0 26.7 1.0
C6 A:5659001 1.3 24.3 1.0
C1 A:5659001 2.4 22.8 1.0
C5 A:5659001 2.4 23.7 1.0
F9 A:5659001 2.8 25.5 1.0
CG2 A:VAL656 3.2 12.6 1.0
CG2 A:VAL711 3.2 16.2 1.0
OG A:SER630 3.5 23.2 1.0
C2 A:5659001 3.6 20.6 1.0
C4 A:5659001 3.7 21.4 1.0
N A:TYR631 3.9 17.3 1.0
C A:SER630 4.0 16.5 1.0
CE1 A:TYR662 4.0 16.2 1.0
CZ A:TYR662 4.1 15.8 1.0
C3 A:5659001 4.2 20.3 1.0
CA A:SER630 4.3 18.1 1.0
OH A:TYR662 4.4 14.6 1.0
CB A:VAL656 4.4 16.6 1.0
CA A:TYR631 4.4 16.8 1.0
CB A:SER630 4.4 17.6 1.0
CD1 A:TYR662 4.4 15.4 1.0
O A:SER630 4.5 17.9 1.0
CE2 A:TYR662 4.5 14.9 1.0
CB A:VAL711 4.6 16.9 1.0
NE2 A:HIS740 4.7 19.3 1.0
F10 A:5659001 4.7 20.7 1.0
CE1 A:HIS740 4.8 17.9 1.0
CB A:TYR631 4.9 17.6 1.0
CG A:TYR662 4.9 16.8 1.0
CD2 A:TYR662 4.9 14.8 1.0
CG1 A:VAL711 4.9 15.2 1.0
N A:VAL656 4.9 17.1 1.0

Fluorine binding site 4 out of 6 in 2iiv

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Fluorine binding site 4 out of 6 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
B:F9002

b:23.1
occ:1.00
 F9 B:5659002 0.0 23.1 1.0
C5 B:5659002 1.3 22.5 1.0
C4 B:5659002 2.4 21.0 1.0
C6 B:5659002 2.4 22.4 1.0
F44 B:5659002 2.7 23.0 1.0
CD2 B:TYR631 3.2 18.9 1.0
OH B:TYR666 3.5 20.4 1.0
CE1 B:TYR666 3.6 20.0 1.0
CB B:TYR631 3.6 19.6 1.0
CZ B:TYR666 3.6 19.9 1.0
C3 B:5659002 3.7 21.6 1.0
C1 B:5659002 3.8 22.1 1.0
CG B:TYR631 3.8 18.9 1.0
CA B:TYR631 4.0 19.2 1.0
CH2 B:TRP659 4.0 16.5 1.0
N B:TYR631 4.2 20.2 1.0
CE2 B:TYR631 4.2 19.4 1.0
C2 B:5659002 4.2 21.1 1.0
CE2 B:TYR662 4.3 15.1 1.0
CZ3 B:TRP659 4.4 15.0 1.0
CD1 B:TYR666 4.4 19.2 1.0
CG2 B:VAL656 4.4 15.8 1.0
CE2 B:TYR666 4.5 19.9 1.0
CZ B:TYR662 4.6 16.9 1.0
OG B:SER630 4.6 24.2 1.0
OH B:TYR547 4.7 20.6 1.0
CD2 B:TYR662 4.8 14.9 1.0
OH B:TYR662 4.9 16.2 1.0
C11 B:5659002 5.0 20.0 1.0

Fluorine binding site 5 out of 6 in 2iiv

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Fluorine binding site 5 out of 6 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
B:F9002

b:20.8
occ:1.00
 F10 B:5659002 0.0 20.8 1.0
C2 B:5659002 1.3 21.1 1.0
C1 B:5659002 2.4 22.1 1.0
C3 B:5659002 2.4 21.6 1.0
C11 B:5659002 2.9 20.0 1.0
ND2 B:ASN710 3.0 18.9 1.0
NH2 B:ARG125 3.2 22.9 1.0
OE2 B:GLU205 3.4 20.0 1.0
N20 B:5659002 3.5 19.0 1.0
CG B:ASN710 3.5 18.3 1.0
OD1 B:ASN710 3.6 18.2 1.0
OH B:TYR662 3.6 16.2 1.0
CD2 B:HIS740 3.6 15.4 1.0
O B:HOH9731 3.6 35.5 1.0
C6 B:5659002 3.7 22.4 1.0
O B:HOH9437 3.8 26.0 1.0
NE2 B:HIS740 3.8 16.3 1.0
C4 B:5659002 3.8 21.0 1.0
C12 B:5659002 3.8 21.5 1.0
OG B:SER630 4.0 24.2 1.0
C5 B:5659002 4.3 22.5 1.0
CZ B:ARG125 4.5 24.0 1.0
CD B:GLU205 4.5 19.9 1.0
C15 B:5659002 4.6 21.5 1.0
CG B:HIS740 4.7 18.1 1.0
CB B:ASN710 4.7 16.9 1.0
F44 B:5659002 4.7 23.0 1.0
CZ B:TYR662 4.7 16.9 1.0
CE1 B:HIS740 4.9 18.2 1.0

Fluorine binding site 6 out of 6 in 2iiv

Go back to Fluorine Binding Sites List in 2iiv
Fluorine binding site 6 out of 6 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
B:F9002

b:23.0
occ:1.00
 F44 B:5659002 0.0 23.0 1.0
C6 B:5659002 1.2 22.4 1.0
C1 B:5659002 2.3 22.1 1.0
C5 B:5659002 2.3 22.5 1.0
F9 B:5659002 2.7 23.1 1.0
CG2 B:VAL656 3.0 15.8 1.0
CG2 B:VAL711 3.2 13.9 1.0
OG B:SER630 3.4 24.2 1.0
C2 B:5659002 3.6 21.1 1.0
C4 B:5659002 3.7 21.0 1.0
N B:TYR631 3.9 20.2 1.0
CE1 B:TYR662 4.0 15.2 1.0
CZ B:TYR662 4.0 16.9 1.0
C B:SER630 4.1 20.1 1.0
C3 B:5659002 4.2 21.6 1.0
OH B:TYR662 4.3 16.2 1.0
CB B:VAL656 4.3 17.9 1.0
CA B:SER630 4.4 20.6 1.0
CA B:TYR631 4.4 19.2 1.0
CD1 B:TYR662 4.4 15.9 1.0
CB B:SER630 4.5 20.1 1.0
CE2 B:TYR662 4.5 15.1 1.0
O B:SER630 4.6 20.4 1.0
CB B:VAL711 4.7 16.0 1.0
NE2 B:HIS740 4.7 16.3 1.0
F10 B:5659002 4.7 20.8 1.0
CE1 B:HIS740 4.8 18.2 1.0
CD2 B:TYR662 4.9 14.9 1.0
CG B:TYR662 4.9 15.3 1.0
CB B:TYR631 4.9 19.6 1.0
N B:VAL656 4.9 17.4 1.0
CG1 B:VAL711 5.0 14.1 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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