Fluorine in PDB 2i78: Crystal Structure of Human Dipeptidyl Peptidase IV (Dpp IV) Complexed with Abt-341, A Cyclohexene-Constrained Phenethylamine Inhibitor
Enzymatic activity of Crystal Structure of Human Dipeptidyl Peptidase IV (Dpp IV) Complexed with Abt-341, A Cyclohexene-Constrained Phenethylamine Inhibitor
All present enzymatic activity of Crystal Structure of Human Dipeptidyl Peptidase IV (Dpp IV) Complexed with Abt-341, A Cyclohexene-Constrained Phenethylamine Inhibitor:
3.4.14.5;
Protein crystallography data
The structure of Crystal Structure of Human Dipeptidyl Peptidase IV (Dpp IV) Complexed with Abt-341, A Cyclohexene-Constrained Phenethylamine Inhibitor, PDB code: 2i78
was solved by
K.L.Longenecker,
Z.Pei,
X.Li,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
129.10 /
2.50
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
119.933,
126.419,
127.531,
90.00,
100.26,
90.00
|
R / Rfree (%)
|
21.6 /
27.5
|
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of Human Dipeptidyl Peptidase IV (Dpp IV) Complexed with Abt-341, A Cyclohexene-Constrained Phenethylamine Inhibitor
(pdb code 2i78). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the
Crystal Structure of Human Dipeptidyl Peptidase IV (Dpp IV) Complexed with Abt-341, A Cyclohexene-Constrained Phenethylamine Inhibitor, PDB code: 2i78:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 2i78
Go back to
Fluorine Binding Sites List in 2i78
Fluorine binding site 1 out
of 6 in the Crystal Structure of Human Dipeptidyl Peptidase IV (Dpp IV) Complexed with Abt-341, A Cyclohexene-Constrained Phenethylamine Inhibitor
 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 Dipeptidyl Peptidase IV (Dpp IV) Complexed with Abt-341, A Cyclohexene-Constrained Phenethylamine Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F901
b:26.0
occ:1.00
|
F31
|
B:KIQ901
|
0.0
|
26.0
|
1.0
|
C30
|
B:KIQ901
|
1.3
|
24.3
|
1.0
|
C29
|
B:KIQ901
|
2.3
|
25.1
|
1.0
|
C23
|
B:KIQ901
|
2.4
|
25.4
|
1.0
|
NH2
|
B:ARG125
|
2.8
|
17.6
|
1.0
|
C22
|
B:KIQ901
|
2.8
|
25.2
|
1.0
|
OE2
|
B:GLU205
|
3.2
|
22.4
|
1.0
|
N
|
B:KIQ901
|
3.4
|
25.3
|
1.0
|
ND2
|
B:ASN710
|
3.4
|
17.1
|
1.0
|
C24
|
B:KIQ901
|
3.6
|
24.9
|
1.0
|
C27
|
B:KIQ901
|
3.6
|
25.5
|
1.0
|
C
|
B:KIQ901
|
3.6
|
25.8
|
1.0
|
OH
|
B:TYR662
|
3.8
|
18.6
|
1.0
|
NE2
|
B:HIS740
|
4.1
|
19.6
|
1.0
|
CZ
|
B:ARG125
|
4.1
|
18.6
|
1.0
|
C21
|
B:KIQ901
|
4.1
|
25.3
|
1.0
|
CD2
|
B:HIS740
|
4.1
|
18.8
|
1.0
|
C25
|
B:KIQ901
|
4.1
|
24.3
|
1.0
|
CG
|
B:ASN710
|
4.2
|
18.3
|
1.0
|
OD1
|
B:ASN710
|
4.2
|
20.1
|
1.0
|
OG
|
B:SER630
|
4.3
|
24.8
|
1.0
|
C3
|
B:KIQ901
|
4.5
|
26.1
|
1.0
|
CD
|
B:GLU205
|
4.5
|
22.7
|
1.0
|
NH1
|
B:ARG125
|
4.7
|
16.3
|
1.0
|
F28
|
B:KIQ901
|
4.7
|
26.2
|
1.0
|
|
Fluorine binding site 2 out
of 6 in 2i78
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Fluorine Binding Sites List in 2i78
Fluorine binding site 2 out
of 6 in the Crystal Structure of Human Dipeptidyl Peptidase IV (Dpp IV) Complexed with Abt-341, A Cyclohexene-Constrained Phenethylamine Inhibitor
 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 Dipeptidyl Peptidase IV (Dpp IV) Complexed with Abt-341, A Cyclohexene-Constrained Phenethylamine Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F901
b:26.2
occ:1.00
|
F28
|
B:KIQ901
|
0.0
|
26.2
|
1.0
|
C27
|
B:KIQ901
|
1.4
|
25.5
|
1.0
|
C25
|
B:KIQ901
|
2.4
|
24.3
|
1.0
|
C29
|
B:KIQ901
|
2.4
|
25.1
|
1.0
|
F26
|
B:KIQ901
|
2.7
|
24.4
|
1.0
|
CG2
|
B:VAL711
|
3.2
|
16.2
|
1.0
|
CG2
|
B:VAL656
|
3.4
|
17.7
|
1.0
|
N
|
B:TYR631
|
3.6
|
22.1
|
1.0
|
C24
|
B:KIQ901
|
3.6
|
24.9
|
1.0
|
C30
|
B:KIQ901
|
3.7
|
24.3
|
1.0
|
C
|
B:SER630
|
3.9
|
22.5
|
1.0
|
OG
|
B:SER630
|
3.9
|
24.8
|
1.0
|
CB
|
B:SER630
|
4.0
|
23.0
|
1.0
|
CA
|
B:SER630
|
4.0
|
22.6
|
1.0
|
C23
|
B:KIQ901
|
4.2
|
25.4
|
1.0
|
CZ
|
B:TYR662
|
4.2
|
18.2
|
1.0
|
OH
|
B:TYR662
|
4.2
|
18.6
|
1.0
|
CE1
|
B:TYR662
|
4.3
|
18.1
|
1.0
|
CA
|
B:TYR631
|
4.4
|
21.5
|
1.0
|
O
|
B:SER630
|
4.5
|
22.6
|
1.0
|
NE2
|
B:HIS740
|
4.5
|
19.6
|
1.0
|
CB
|
B:VAL656
|
4.6
|
19.4
|
1.0
|
CE1
|
B:HIS740
|
4.6
|
19.3
|
1.0
|
CE2
|
B:TYR662
|
4.6
|
18.3
|
1.0
|
CB
|
B:VAL711
|
4.6
|
15.9
|
1.0
|
F31
|
B:KIQ901
|
4.7
|
26.0
|
1.0
|
N
|
B:VAL656
|
4.8
|
19.8
|
1.0
|
CB
|
B:TYR631
|
4.8
|
21.5
|
1.0
|
CD1
|
B:TYR662
|
4.8
|
18.4
|
1.0
|
CG1
|
B:VAL711
|
4.9
|
15.4
|
1.0
|
O
|
B:ALA654
|
5.0
|
20.9
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 2i78
Go back to
Fluorine Binding Sites List in 2i78
Fluorine binding site 3 out
of 6 in the Crystal Structure of Human Dipeptidyl Peptidase IV (Dpp IV) Complexed with Abt-341, A Cyclohexene-Constrained Phenethylamine Inhibitor
 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 Dipeptidyl Peptidase IV (Dpp IV) Complexed with Abt-341, A Cyclohexene-Constrained Phenethylamine Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F901
b:24.4
occ:1.00
|
F26
|
B:KIQ901
|
0.0
|
24.4
|
1.0
|
C25
|
B:KIQ901
|
1.3
|
24.3
|
1.0
|
C27
|
B:KIQ901
|
2.3
|
25.5
|
1.0
|
C24
|
B:KIQ901
|
2.4
|
24.9
|
1.0
|
F28
|
B:KIQ901
|
2.7
|
26.2
|
1.0
|
CD2
|
B:TYR631
|
3.5
|
21.2
|
1.0
|
CE1
|
B:TYR666
|
3.5
|
16.9
|
1.0
|
C29
|
B:KIQ901
|
3.6
|
25.1
|
1.0
|
C23
|
B:KIQ901
|
3.6
|
25.4
|
1.0
|
CZ
|
B:TYR666
|
3.6
|
17.5
|
1.0
|
OH
|
B:TYR666
|
3.7
|
18.8
|
1.0
|
CB
|
B:TYR631
|
3.7
|
21.5
|
1.0
|
CG
|
B:TYR631
|
4.1
|
20.4
|
1.0
|
CH2
|
B:TRP659
|
4.1
|
18.1
|
1.0
|
C30
|
B:KIQ901
|
4.1
|
24.3
|
1.0
|
CA
|
B:TYR631
|
4.1
|
21.5
|
1.0
|
N
|
B:TYR631
|
4.2
|
22.1
|
1.0
|
CE2
|
B:TYR662
|
4.2
|
18.3
|
1.0
|
CD1
|
B:TYR666
|
4.2
|
17.0
|
1.0
|
CZ3
|
B:TRP659
|
4.3
|
17.9
|
1.0
|
CG2
|
B:VAL656
|
4.3
|
17.7
|
1.0
|
CE2
|
B:TYR666
|
4.4
|
15.8
|
1.0
|
CZ
|
B:TYR662
|
4.5
|
18.2
|
1.0
|
CE2
|
B:TYR631
|
4.5
|
21.3
|
1.0
|
OH
|
B:TYR662
|
4.7
|
18.6
|
1.0
|
CD2
|
B:TYR662
|
4.7
|
18.8
|
1.0
|
C22
|
B:KIQ901
|
4.9
|
25.2
|
1.0
|
CG
|
B:TYR666
|
4.9
|
18.0
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 2i78
Go back to
Fluorine Binding Sites List in 2i78
Fluorine binding site 4 out
of 6 in the Crystal Structure of Human Dipeptidyl Peptidase IV (Dpp IV) Complexed with Abt-341, A Cyclohexene-Constrained Phenethylamine Inhibitor
 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 Dipeptidyl Peptidase IV (Dpp IV) Complexed with Abt-341, A Cyclohexene-Constrained Phenethylamine Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F901
b:46.2
occ:1.00
|
F19
|
B:KIQ901
|
0.0
|
46.2
|
1.0
|
C16
|
B:KIQ901
|
1.3
|
44.5
|
1.0
|
F
|
B:KIQ901
|
2.2
|
46.4
|
1.0
|
F18
|
B:KIQ901
|
2.2
|
45.9
|
1.0
|
C15
|
B:KIQ901
|
2.3
|
43.7
|
1.0
|
N10
|
B:KIQ901
|
3.1
|
42.7
|
1.0
|
OH
|
B:TYR585
|
3.2
|
25.5
|
1.0
|
N14
|
B:KIQ901
|
3.2
|
43.1
|
1.0
|
CE2
|
B:PHE357
|
3.5
|
23.5
|
1.0
|
C9
|
B:KIQ901
|
3.6
|
39.3
|
1.0
|
CZ
|
B:PHE357
|
4.0
|
23.9
|
1.0
|
C11
|
B:KIQ901
|
4.2
|
41.6
|
1.0
|
N13
|
B:KIQ901
|
4.3
|
42.8
|
1.0
|
CD2
|
B:PHE357
|
4.5
|
22.4
|
1.0
|
CZ
|
B:TYR585
|
4.5
|
24.0
|
1.0
|
O
|
B:CYS551
|
4.7
|
23.7
|
1.0
|
|
Fluorine binding site 5 out
of 6 in 2i78
Go back to
Fluorine Binding Sites List in 2i78
Fluorine binding site 5 out
of 6 in the Crystal Structure of Human Dipeptidyl Peptidase IV (Dpp IV) Complexed with Abt-341, A Cyclohexene-Constrained Phenethylamine Inhibitor
 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 Dipeptidyl Peptidase IV (Dpp IV) Complexed with Abt-341, A Cyclohexene-Constrained Phenethylamine Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F901
b:45.9
occ:1.00
|
F18
|
B:KIQ901
|
0.0
|
45.9
|
1.0
|
C16
|
B:KIQ901
|
1.3
|
44.5
|
1.0
|
F
|
B:KIQ901
|
2.1
|
46.4
|
1.0
|
F19
|
B:KIQ901
|
2.2
|
46.2
|
1.0
|
C15
|
B:KIQ901
|
2.3
|
43.7
|
1.0
|
N10
|
B:KIQ901
|
2.9
|
42.7
|
1.0
|
C9
|
B:KIQ901
|
3.0
|
39.3
|
1.0
|
N14
|
B:KIQ901
|
3.5
|
43.1
|
1.0
|
C11
|
B:KIQ901
|
4.1
|
41.6
|
1.0
|
C8
|
B:KIQ901
|
4.4
|
36.6
|
1.0
|
N13
|
B:KIQ901
|
4.4
|
42.8
|
1.0
|
OH
|
B:TYR585
|
4.9
|
25.5
|
1.0
|
|
Fluorine binding site 6 out
of 6 in 2i78
Go back to
Fluorine Binding Sites List in 2i78
Fluorine binding site 6 out
of 6 in the Crystal Structure of Human Dipeptidyl Peptidase IV (Dpp IV) Complexed with Abt-341, A Cyclohexene-Constrained Phenethylamine Inhibitor
 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 Dipeptidyl Peptidase IV (Dpp IV) Complexed with Abt-341, A Cyclohexene-Constrained Phenethylamine Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F901
b:46.4
occ:1.00
|
F
|
B:KIQ901
|
0.0
|
46.4
|
1.0
|
C16
|
B:KIQ901
|
1.3
|
44.5
|
1.0
|
F18
|
B:KIQ901
|
2.1
|
45.9
|
1.0
|
F19
|
B:KIQ901
|
2.2
|
46.2
|
1.0
|
C15
|
B:KIQ901
|
2.3
|
43.7
|
1.0
|
N14
|
B:KIQ901
|
2.6
|
43.1
|
1.0
|
N10
|
B:KIQ901
|
3.5
|
42.7
|
1.0
|
OH
|
B:TYR585
|
3.6
|
25.5
|
1.0
|
N13
|
B:KIQ901
|
3.9
|
42.8
|
1.0
|
C11
|
B:KIQ901
|
4.3
|
41.6
|
1.0
|
C9
|
B:KIQ901
|
4.4
|
39.3
|
1.0
|
CE2
|
B:PHE357
|
4.9
|
23.5
|
1.0
|
CZ
|
B:TYR585
|
5.0
|
24.0
|
1.0
|
|
Reference:
Z.Pei,
X.Li,
T.W.Vongeldern,
D.J.Madar,
K.L Longenecker,
H.Yong,
T.H.Lubben,
K.D.Stewart,
B.A.Zinker,
B.J.Backes,
A.S.Judd,
M.Mulhern,
S.J.Ballaron,
M.A.Stashko,
A.K.Mika,
D.W.A.Beno,
G.A.Reinhart,
R.M.Fryer,
L.C.Preusser,
A.J.Kempf-Grote,
H.L.Sham,
J.M.Trevillyan.
Discovery of Cyclohexene-Constrained Phenethylamine Abt-341, A Highly Potent, Selective, Orally Bioavailable, Safe and Potential Next-Generation Dipeptidyl Peptidase IV Inhibitor For the Treatment of Type 2 Diabetes To Be Published.
Page generated: Wed Jul 31 14:50:35 2024
|