Fluorine in PDB 3d4l: Human Dipeptidyl Peptidase IV/CD26 in Complex with A Novel Inhibitor
Enzymatic activity of Human Dipeptidyl Peptidase IV/CD26 in Complex with A Novel Inhibitor
All present enzymatic activity of Human Dipeptidyl Peptidase IV/CD26 in Complex with A Novel Inhibitor:
3.4.14.5;
Protein crystallography data
The structure of Human Dipeptidyl Peptidase IV/CD26 in Complex with A Novel Inhibitor, PDB code: 3d4l
was solved by
G.Scapin,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
30.00 /
2.00
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
118.435,
125.749,
137.175,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
n/a /
n/a
|
Other elements in 3d4l:
The structure of Human Dipeptidyl Peptidase IV/CD26 in Complex with A Novel Inhibitor also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Human Dipeptidyl Peptidase IV/CD26 in Complex with A Novel Inhibitor
(pdb code 3d4l). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the
Human Dipeptidyl Peptidase IV/CD26 in Complex with A Novel Inhibitor, PDB code: 3d4l:
Jump to Fluorine binding site number:
1;
2;
3;
4;
Fluorine binding site 1 out
of 4 in 3d4l
Go back to
Fluorine Binding Sites List in 3d4l
Fluorine binding site 1 out
of 4 in the Human Dipeptidyl Peptidase IV/CD26 in Complex with A Novel 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 Novel Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1521
b:25.3
occ:1.00
|
F34
|
A:6051521
|
0.0
|
25.3
|
1.0
|
C5
|
A:6051521
|
1.3
|
24.7
|
1.0
|
C6
|
A:6051521
|
2.4
|
23.8
|
1.0
|
C4
|
A:6051521
|
2.4
|
22.5
|
1.0
|
CD2
|
A:TYR631
|
3.5
|
22.6
|
1.0
|
CH2
|
A:TRP659
|
3.6
|
20.5
|
1.0
|
C1
|
A:6051521
|
3.7
|
22.9
|
1.0
|
C3
|
A:6051521
|
3.7
|
22.4
|
1.0
|
CE1
|
A:TYR666
|
3.7
|
20.5
|
1.0
|
CB
|
A:TYR631
|
3.8
|
21.4
|
1.0
|
CG2
|
A:VAL656
|
3.8
|
19.6
|
1.0
|
OH
|
A:TYR666
|
3.9
|
22.7
|
1.0
|
CZ3
|
A:TRP659
|
3.9
|
19.9
|
1.0
|
CZ
|
A:TYR666
|
3.9
|
21.9
|
1.0
|
CA
|
A:TYR631
|
4.1
|
21.5
|
1.0
|
CG
|
A:TYR631
|
4.1
|
22.2
|
1.0
|
C2
|
A:6051521
|
4.2
|
22.4
|
1.0
|
CE2
|
A:TYR662
|
4.2
|
20.5
|
1.0
|
N
|
A:TYR631
|
4.2
|
21.1
|
1.0
|
CE2
|
A:TYR631
|
4.5
|
23.7
|
1.0
|
CZ
|
A:TYR662
|
4.5
|
20.8
|
1.0
|
CD2
|
A:TYR662
|
4.5
|
20.0
|
1.0
|
CD1
|
A:TYR666
|
4.5
|
21.2
|
1.0
|
OG
|
A:SER630
|
4.7
|
26.1
|
1.0
|
OH
|
A:TYR662
|
4.8
|
21.2
|
1.0
|
CE2
|
A:TYR666
|
4.8
|
22.4
|
1.0
|
CB
|
A:VAL656
|
4.9
|
21.4
|
1.0
|
CZ2
|
A:TRP659
|
4.9
|
20.8
|
1.0
|
C10
|
A:6051521
|
4.9
|
22.0
|
1.0
|
CE1
|
A:TYR662
|
4.9
|
21.0
|
1.0
|
CG
|
A:TYR662
|
5.0
|
21.2
|
1.0
|
|
Fluorine binding site 2 out
of 4 in 3d4l
Go back to
Fluorine Binding Sites List in 3d4l
Fluorine binding site 2 out
of 4 in the Human Dipeptidyl Peptidase IV/CD26 in Complex with A Novel 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 Novel Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1521
b:23.1
occ:1.00
|
F35
|
A:6051521
|
0.0
|
23.1
|
1.0
|
C2
|
A:6051521
|
1.3
|
22.4
|
1.0
|
C1
|
A:6051521
|
2.3
|
22.9
|
1.0
|
C3
|
A:6051521
|
2.4
|
22.4
|
1.0
|
C10
|
A:6051521
|
2.9
|
22.0
|
1.0
|
ND2
|
A:ASN710
|
3.1
|
21.3
|
1.0
|
NH2
|
A:ARG125
|
3.2
|
24.0
|
1.0
|
OE2
|
A:GLU205
|
3.3
|
21.7
|
1.0
|
N15
|
A:6051521
|
3.4
|
17.7
|
1.0
|
O
|
A:HOH1574
|
3.6
|
27.8
|
1.0
|
OH
|
A:TYR662
|
3.6
|
21.2
|
1.0
|
OD1
|
A:ASN710
|
3.6
|
22.6
|
1.0
|
CG
|
A:ASN710
|
3.6
|
22.4
|
1.0
|
C6
|
A:6051521
|
3.6
|
23.8
|
1.0
|
C4
|
A:6051521
|
3.7
|
22.5
|
1.0
|
NE2
|
A:HIS740
|
3.8
|
25.1
|
1.0
|
O
|
A:HOH1710
|
3.8
|
38.5
|
1.0
|
C11
|
A:6051521
|
3.8
|
20.2
|
1.0
|
CD2
|
A:HIS740
|
3.8
|
25.7
|
1.0
|
OG
|
A:SER630
|
3.8
|
26.1
|
1.0
|
C5
|
A:6051521
|
4.1
|
24.7
|
1.0
|
CD
|
A:GLU205
|
4.5
|
22.9
|
1.0
|
CZ
|
A:ARG125
|
4.5
|
25.1
|
1.0
|
CZ
|
A:TYR662
|
4.7
|
20.8
|
1.0
|
CB
|
A:ASN710
|
4.8
|
21.9
|
1.0
|
CE1
|
A:HIS740
|
4.8
|
26.1
|
1.0
|
C14
|
A:6051521
|
4.8
|
20.6
|
1.0
|
CG
|
A:HIS740
|
4.8
|
25.5
|
1.0
|
|
Fluorine binding site 3 out
of 4 in 3d4l
Go back to
Fluorine Binding Sites List in 3d4l
Fluorine binding site 3 out
of 4 in the Human Dipeptidyl Peptidase IV/CD26 in Complex with A Novel 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 Novel Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F1521
b:25.1
occ:1.00
|
F34
|
B:6051521
|
0.0
|
25.1
|
1.0
|
C5
|
B:6051521
|
1.3
|
23.9
|
1.0
|
C4
|
B:6051521
|
2.3
|
23.3
|
1.0
|
C6
|
B:6051521
|
2.4
|
22.1
|
1.0
|
CD2
|
B:TYR631
|
3.5
|
24.3
|
1.0
|
C3
|
B:6051521
|
3.7
|
23.4
|
1.0
|
C1
|
B:6051521
|
3.7
|
22.4
|
1.0
|
CH2
|
B:TRP659
|
3.8
|
23.9
|
1.0
|
CG2
|
B:VAL656
|
3.8
|
21.1
|
1.0
|
CE1
|
B:TYR666
|
3.8
|
23.9
|
1.0
|
CB
|
B:TYR631
|
3.8
|
23.4
|
1.0
|
OH
|
B:TYR666
|
4.0
|
24.2
|
1.0
|
CZ
|
B:TYR666
|
4.0
|
24.4
|
1.0
|
CA
|
B:TYR631
|
4.1
|
24.1
|
1.0
|
CZ3
|
B:TRP659
|
4.1
|
23.2
|
1.0
|
CG
|
B:TYR631
|
4.1
|
23.6
|
1.0
|
C2
|
B:6051521
|
4.1
|
23.1
|
1.0
|
CE2
|
B:TYR662
|
4.2
|
21.2
|
1.0
|
N
|
B:TYR631
|
4.2
|
24.4
|
1.0
|
CZ
|
B:TYR662
|
4.4
|
23.0
|
1.0
|
CE2
|
B:TYR631
|
4.5
|
24.1
|
1.0
|
CD1
|
B:TYR666
|
4.5
|
24.2
|
1.0
|
CD2
|
B:TYR662
|
4.5
|
20.7
|
1.0
|
OG
|
B:SER630
|
4.6
|
27.7
|
1.0
|
CB
|
B:VAL656
|
4.8
|
22.0
|
1.0
|
OH
|
B:TYR662
|
4.8
|
22.8
|
1.0
|
CE2
|
B:TYR666
|
4.9
|
23.9
|
1.0
|
C10
|
B:6051521
|
4.9
|
23.4
|
1.0
|
CE1
|
B:TYR662
|
4.9
|
22.9
|
1.0
|
CZ2
|
B:TRP659
|
5.0
|
24.1
|
1.0
|
|
Fluorine binding site 4 out
of 4 in 3d4l
Go back to
Fluorine Binding Sites List in 3d4l
Fluorine binding site 4 out
of 4 in the Human Dipeptidyl Peptidase IV/CD26 in Complex with A Novel 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 Novel Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F1521
b:23.8
occ:1.00
|
F35
|
B:6051521
|
0.0
|
23.8
|
1.0
|
C2
|
B:6051521
|
1.3
|
23.1
|
1.0
|
C3
|
B:6051521
|
2.4
|
23.4
|
1.0
|
C1
|
B:6051521
|
2.4
|
22.4
|
1.0
|
C10
|
B:6051521
|
2.9
|
23.4
|
1.0
|
NH2
|
B:ARG125
|
3.0
|
25.2
|
1.0
|
ND2
|
B:ASN710
|
3.3
|
21.9
|
1.0
|
OE2
|
B:GLU205
|
3.3
|
25.2
|
1.0
|
N15
|
B:6051521
|
3.4
|
22.0
|
1.0
|
OD1
|
B:ASN710
|
3.5
|
20.0
|
1.0
|
OH
|
B:TYR662
|
3.6
|
22.8
|
1.0
|
O
|
B:HOH2456
|
3.6
|
29.5
|
1.0
|
CG
|
B:ASN710
|
3.6
|
22.5
|
1.0
|
C6
|
B:6051521
|
3.7
|
22.1
|
1.0
|
C4
|
B:6051521
|
3.7
|
23.3
|
1.0
|
CD2
|
B:HIS740
|
3.8
|
22.1
|
1.0
|
O
|
B:HOH2556
|
3.8
|
40.5
|
1.0
|
C11
|
B:6051521
|
3.8
|
23.5
|
1.0
|
NE2
|
B:HIS740
|
3.8
|
22.1
|
1.0
|
OG
|
B:SER630
|
3.9
|
27.7
|
1.0
|
C5
|
B:6051521
|
4.1
|
23.9
|
1.0
|
CZ
|
B:ARG125
|
4.4
|
24.7
|
1.0
|
CD
|
B:GLU205
|
4.5
|
24.4
|
1.0
|
CZ
|
B:TYR662
|
4.7
|
23.0
|
1.0
|
C14
|
B:6051521
|
4.8
|
24.9
|
1.0
|
CG
|
B:HIS740
|
4.9
|
22.6
|
1.0
|
CE1
|
B:HIS740
|
4.9
|
22.6
|
1.0
|
CB
|
B:ASN710
|
4.9
|
22.3
|
1.0
|
|
Reference:
G.B.Liang,
X.Qian,
T.Biftu,
S.Singh,
Y.D.Gao,
G.Scapin,
S.Patel,
B.Leiting,
R.Patel,
J.Wu,
X.Zhang,
N.A.Thornberry,
A.E.Weber.
Discovery of New Binding Elements in Dpp-4 Inhibition and Their Applications in Novel Dpp-4 Inhibitor Design. Bioorg.Med.Chem.Lett. V. 18 3706 2008.
ISSN: ISSN 0960-894X
PubMed: 18524582
DOI: 10.1016/J.BMCL.2008.05.061
Page generated: Wed Jul 31 17:51:31 2024
|