Fluorine in PDB 2buc: Crystal Structure of Porcine Dipeptidyl Peptidase IV (CD26) in Complex with A Tetrahydroisoquinoline Inhibitor
Enzymatic activity of Crystal Structure of Porcine Dipeptidyl Peptidase IV (CD26) in Complex with A Tetrahydroisoquinoline Inhibitor
All present enzymatic activity of Crystal Structure of Porcine Dipeptidyl Peptidase IV (CD26) in Complex with A Tetrahydroisoquinoline Inhibitor:
3.4.14.5;
Protein crystallography data
The structure of Crystal Structure of Porcine Dipeptidyl Peptidase IV (CD26) in Complex with A Tetrahydroisoquinoline Inhibitor, PDB code: 2buc
was solved by
S.Nordhoff,
S.Cerezo-Galvez,
A.Feurer,
O.Hill,
V.G.Matassa,
G.Metz,
C.Rummey,
M.Thiemann,
P.J.Edwards,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.28 /
2.50
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
61.644,
117.491,
133.057,
112.44,
94.72,
91.30
|
R / Rfree (%)
|
22.1 /
27.9
|
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of Porcine Dipeptidyl Peptidase IV (CD26) in Complex with A Tetrahydroisoquinoline Inhibitor
(pdb code 2buc). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the
Crystal Structure of Porcine Dipeptidyl Peptidase IV (CD26) in Complex with A Tetrahydroisoquinoline Inhibitor, PDB code: 2buc:
Jump to Fluorine binding site number:
1;
2;
3;
4;
Fluorine binding site 1 out
of 4 in 2buc
Go back to
Fluorine Binding Sites List in 2buc
Fluorine binding site 1 out
of 4 in the Crystal Structure of Porcine Dipeptidyl Peptidase IV (CD26) in Complex with A Tetrahydroisoquinoline 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 Porcine Dipeptidyl Peptidase IV (CD26) in Complex with A Tetrahydroisoquinoline Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1767
b:43.1
occ:1.00
|
F7
|
A:0081767
|
0.0
|
43.1
|
1.0
|
C1
|
A:0081767
|
1.3
|
43.3
|
1.0
|
C2
|
A:0081767
|
2.4
|
43.2
|
1.0
|
C6
|
A:0081767
|
2.4
|
43.2
|
1.0
|
C8
|
A:0081767
|
2.8
|
43.6
|
1.0
|
ND2
|
A:ASN710
|
3.1
|
36.5
|
1.0
|
OH
|
A:TYR662
|
3.1
|
37.1
|
1.0
|
NE2
|
A:HIS740
|
3.3
|
44.7
|
1.0
|
OD1
|
A:ASN710
|
3.4
|
36.2
|
1.0
|
CG
|
A:ASN710
|
3.4
|
36.3
|
1.0
|
O3
|
A:SO41769
|
3.5
|
62.1
|
1.0
|
NH2
|
A:ARG125
|
3.5
|
48.1
|
1.0
|
N10
|
A:0081767
|
3.6
|
43.1
|
1.0
|
C3
|
A:0081767
|
3.6
|
43.1
|
1.0
|
C5
|
A:0081767
|
3.6
|
43.2
|
1.0
|
CD2
|
A:HIS740
|
3.7
|
45.0
|
1.0
|
O2
|
A:SO41769
|
3.8
|
62.1
|
1.0
|
OE2
|
A:GLU205
|
3.8
|
39.4
|
1.0
|
C9
|
A:0081767
|
3.8
|
43.9
|
1.0
|
S
|
A:SO41769
|
4.1
|
62.3
|
1.0
|
C4
|
A:0081767
|
4.1
|
43.5
|
1.0
|
CZ
|
A:TYR662
|
4.2
|
37.6
|
1.0
|
CE1
|
A:HIS740
|
4.3
|
45.0
|
1.0
|
O4
|
A:SO41769
|
4.4
|
62.6
|
1.0
|
CB
|
A:SER630
|
4.5
|
48.8
|
1.0
|
CG2
|
A:VAL711
|
4.5
|
36.0
|
1.0
|
OG
|
A:SER630
|
4.5
|
49.5
|
1.0
|
CB
|
A:ASN710
|
4.6
|
36.4
|
1.0
|
CE1
|
A:TYR662
|
4.7
|
37.9
|
1.0
|
CG
|
A:HIS740
|
4.8
|
45.8
|
1.0
|
CZ
|
A:ARG125
|
4.8
|
48.1
|
1.0
|
CD
|
A:GLU205
|
4.9
|
39.9
|
1.0
|
C11
|
A:0081767
|
5.0
|
44.6
|
1.0
|
|
Fluorine binding site 2 out
of 4 in 2buc
Go back to
Fluorine Binding Sites List in 2buc
Fluorine binding site 2 out
of 4 in the Crystal Structure of Porcine Dipeptidyl Peptidase IV (CD26) in Complex with A Tetrahydroisoquinoline 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 Porcine Dipeptidyl Peptidase IV (CD26) in Complex with A Tetrahydroisoquinoline Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F1767
b:36.5
occ:1.00
|
F7
|
B:0081767
|
0.0
|
36.5
|
1.0
|
C1
|
B:0081767
|
1.3
|
36.8
|
1.0
|
C2
|
B:0081767
|
2.4
|
37.3
|
1.0
|
C6
|
B:0081767
|
2.4
|
37.6
|
1.0
|
C8
|
B:0081767
|
2.8
|
38.3
|
1.0
|
OH
|
B:TYR662
|
3.2
|
37.3
|
1.0
|
OD1
|
B:ASN710
|
3.3
|
36.7
|
1.0
|
O1
|
B:SO41769
|
3.3
|
73.5
|
1.0
|
NE2
|
B:HIS740
|
3.3
|
44.9
|
1.0
|
ND2
|
B:ASN710
|
3.4
|
36.5
|
1.0
|
NH2
|
B:ARG125
|
3.5
|
46.9
|
1.0
|
N10
|
B:0081767
|
3.5
|
38.4
|
1.0
|
CG
|
B:ASN710
|
3.5
|
36.4
|
1.0
|
O3
|
B:SO41769
|
3.6
|
73.7
|
1.0
|
CD2
|
B:HIS740
|
3.6
|
45.4
|
1.0
|
OE2
|
B:GLU205
|
3.6
|
40.1
|
1.0
|
C3
|
B:0081767
|
3.6
|
38.0
|
1.0
|
C5
|
B:0081767
|
3.6
|
37.5
|
1.0
|
C9
|
B:0081767
|
3.8
|
39.1
|
1.0
|
S
|
B:SO41769
|
4.0
|
74.0
|
1.0
|
C4
|
B:0081767
|
4.1
|
37.9
|
1.0
|
CZ
|
B:TYR662
|
4.2
|
37.5
|
1.0
|
CE1
|
B:HIS740
|
4.4
|
44.9
|
1.0
|
O4
|
B:SO41769
|
4.5
|
74.1
|
1.0
|
CB
|
B:SER630
|
4.6
|
46.7
|
1.0
|
OG
|
B:SER630
|
4.6
|
47.0
|
1.0
|
CG2
|
B:VAL711
|
4.7
|
36.1
|
1.0
|
CB
|
B:ASN710
|
4.7
|
36.4
|
1.0
|
CD
|
B:GLU205
|
4.7
|
39.8
|
1.0
|
CG
|
B:HIS740
|
4.7
|
45.8
|
1.0
|
CE1
|
B:TYR662
|
4.7
|
37.4
|
1.0
|
CZ
|
B:ARG125
|
4.8
|
47.5
|
1.0
|
C11
|
B:0081767
|
4.9
|
40.2
|
1.0
|
|
Fluorine binding site 3 out
of 4 in 2buc
Go back to
Fluorine Binding Sites List in 2buc
Fluorine binding site 3 out
of 4 in the Crystal Structure of Porcine Dipeptidyl Peptidase IV (CD26) in Complex with A Tetrahydroisoquinoline 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 Porcine Dipeptidyl Peptidase IV (CD26) in Complex with A Tetrahydroisoquinoline Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F1767
b:42.3
occ:1.00
|
F7
|
C:0081767
|
0.0
|
42.3
|
1.0
|
C1
|
C:0081767
|
1.3
|
41.3
|
1.0
|
C2
|
C:0081767
|
2.4
|
41.2
|
1.0
|
C6
|
C:0081767
|
2.4
|
41.4
|
1.0
|
C8
|
C:0081767
|
2.8
|
41.1
|
1.0
|
OD1
|
C:ASN710
|
3.0
|
37.0
|
1.0
|
OH
|
C:TYR662
|
3.1
|
36.9
|
1.0
|
NE2
|
C:HIS740
|
3.4
|
44.6
|
1.0
|
N10
|
C:0081767
|
3.4
|
41.6
|
1.0
|
O2
|
C:SO41769
|
3.4
|
70.7
|
1.0
|
NH2
|
C:ARG125
|
3.5
|
48.8
|
1.0
|
CG
|
C:ASN710
|
3.5
|
36.6
|
1.0
|
ND2
|
C:ASN710
|
3.5
|
37.0
|
1.0
|
OE2
|
C:GLU205
|
3.6
|
38.6
|
1.0
|
CD2
|
C:HIS740
|
3.6
|
45.0
|
1.0
|
C3
|
C:0081767
|
3.6
|
41.5
|
1.0
|
C5
|
C:0081767
|
3.6
|
41.6
|
1.0
|
C9
|
C:0081767
|
3.7
|
42.0
|
1.0
|
O4
|
C:SO41769
|
3.8
|
70.8
|
1.0
|
S
|
C:SO41769
|
4.0
|
70.8
|
1.0
|
C4
|
C:0081767
|
4.1
|
41.5
|
1.0
|
O1
|
C:SO41769
|
4.1
|
70.7
|
1.0
|
CZ
|
C:TYR662
|
4.1
|
37.7
|
1.0
|
CE1
|
C:HIS740
|
4.4
|
44.7
|
1.0
|
CB
|
C:SER630
|
4.6
|
46.2
|
1.0
|
CE1
|
C:TYR662
|
4.6
|
37.7
|
1.0
|
OG
|
C:SER630
|
4.7
|
47.1
|
1.0
|
CB
|
C:ASN710
|
4.7
|
36.4
|
1.0
|
CG2
|
C:VAL711
|
4.7
|
36.1
|
1.0
|
CD
|
C:GLU205
|
4.7
|
38.7
|
1.0
|
CG
|
C:HIS740
|
4.8
|
45.6
|
1.0
|
CZ
|
C:ARG125
|
4.8
|
48.8
|
1.0
|
C11
|
C:0081767
|
4.9
|
42.8
|
1.0
|
|
Fluorine binding site 4 out
of 4 in 2buc
Go back to
Fluorine Binding Sites List in 2buc
Fluorine binding site 4 out
of 4 in the Crystal Structure of Porcine Dipeptidyl Peptidase IV (CD26) in Complex with A Tetrahydroisoquinoline 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 Porcine Dipeptidyl Peptidase IV (CD26) in Complex with A Tetrahydroisoquinoline Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F1767
b:50.0
occ:1.00
|
F7
|
D:0081767
|
0.0
|
50.0
|
1.0
|
C1
|
D:0081767
|
1.3
|
50.2
|
1.0
|
C2
|
D:0081767
|
2.4
|
49.9
|
1.0
|
C6
|
D:0081767
|
2.4
|
50.5
|
1.0
|
C8
|
D:0081767
|
2.8
|
51.2
|
1.0
|
OH
|
D:TYR662
|
3.0
|
37.6
|
1.0
|
OD1
|
D:ASN710
|
3.2
|
36.8
|
1.0
|
ND2
|
D:ASN710
|
3.4
|
36.8
|
1.0
|
O4
|
D:SO41769
|
3.4
|
66.5
|
1.0
|
NE2
|
D:HIS740
|
3.4
|
44.9
|
1.0
|
O2
|
D:SO41769
|
3.5
|
66.6
|
1.0
|
N10
|
D:0081767
|
3.5
|
52.0
|
1.0
|
CG
|
D:ASN710
|
3.6
|
36.6
|
1.0
|
C3
|
D:0081767
|
3.6
|
50.2
|
1.0
|
C5
|
D:0081767
|
3.6
|
50.4
|
1.0
|
NH2
|
D:ARG125
|
3.7
|
48.8
|
1.0
|
OE2
|
D:GLU205
|
3.7
|
41.1
|
1.0
|
CD2
|
D:HIS740
|
3.7
|
45.2
|
1.0
|
C9
|
D:0081767
|
3.8
|
52.0
|
1.0
|
S
|
D:SO41769
|
4.0
|
66.9
|
1.0
|
CZ
|
D:TYR662
|
4.1
|
37.6
|
1.0
|
C4
|
D:0081767
|
4.1
|
50.3
|
1.0
|
CB
|
D:SER630
|
4.4
|
50.3
|
1.0
|
CE1
|
D:HIS740
|
4.4
|
45.1
|
1.0
|
OG
|
D:SER630
|
4.6
|
50.8
|
1.0
|
CG2
|
D:VAL711
|
4.6
|
36.2
|
1.0
|
CE1
|
D:TYR662
|
4.6
|
37.6
|
1.0
|
O1
|
D:SO41769
|
4.8
|
66.5
|
1.0
|
CB
|
D:ASN710
|
4.8
|
36.6
|
1.0
|
CD
|
D:GLU205
|
4.8
|
41.1
|
1.0
|
CG
|
D:HIS740
|
4.8
|
45.8
|
1.0
|
C11
|
D:0081767
|
4.9
|
52.6
|
1.0
|
CZ
|
D:ARG125
|
5.0
|
49.0
|
1.0
|
|
Reference:
S.Nordhoff,
S.Cerezo-Galvez,
A.Feurer,
O.Hill,
V.G.Matassa,
G.Metz,
C.Rummey,
M.Thiemann,
P.J.Edwards.
The Reversed Binding of Beta-Phenethylamine Inhibitors of Dpp-IV: X-Ray Structures and Properties of Novel Fragment and Elaborated Inhibitors. Bioorg. Med. Chem. Lett. V. 16 1744 2006.
ISSN: ISSN 0960-894X
PubMed: 16376544
DOI: 10.1016/J.BMCL.2005.11.103
Page generated: Wed Jul 31 13:53:20 2024
|