Bromine in PDB 4g1f: Crystal Structure of Human Dipeptidyl Peptidase IV in Complex with A Pyridopyrimidinedione Analogue
Enzymatic activity of Crystal Structure of Human Dipeptidyl Peptidase IV in Complex with A Pyridopyrimidinedione Analogue
All present enzymatic activity of Crystal Structure of Human Dipeptidyl Peptidase IV in Complex with A Pyridopyrimidinedione Analogue:
3.4.14.5;
Protein crystallography data
The structure of Crystal Structure of Human Dipeptidyl Peptidase IV in Complex with A Pyridopyrimidinedione Analogue, PDB code: 4g1f
was solved by
R.J.Skene,
S.L.Gwaltney,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
40.00 /
2.90
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
121.622,
121.362,
143.257,
90.00,
114.63,
90.00
|
R / Rfree (%)
|
20.7 /
25.9
|
Bromine Binding Sites:
The binding sites of Bromine atom in the Crystal Structure of Human Dipeptidyl Peptidase IV in Complex with A Pyridopyrimidinedione Analogue
(pdb code 4g1f). This binding sites where shown within
5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the
Crystal Structure of Human Dipeptidyl Peptidase IV in Complex with A Pyridopyrimidinedione Analogue, PDB code: 4g1f:
Jump to Bromine binding site number:
1;
2;
3;
4;
Bromine binding site 1 out
of 4 in 4g1f
Go back to
Bromine Binding Sites List in 4g1f
Bromine binding site 1 out
of 4 in the Crystal Structure of Human Dipeptidyl Peptidase IV in Complex with A Pyridopyrimidinedione Analogue
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 1 of Crystal Structure of Human Dipeptidyl Peptidase IV in Complex with A Pyridopyrimidinedione Analogue within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Br800
b:39.4
occ:1.00
|
BR1
|
A:0WG800
|
0.0
|
39.4
|
1.0
|
C16
|
A:0WG800
|
1.9
|
32.8
|
1.0
|
C15
|
A:0WG800
|
2.8
|
31.9
|
1.0
|
C11
|
A:0WG800
|
2.9
|
31.5
|
1.0
|
C10
|
A:0WG800
|
3.1
|
30.1
|
1.0
|
O
|
A:HOH955
|
3.3
|
31.4
|
1.0
|
C18
|
A:0WG800
|
3.5
|
29.0
|
1.0
|
OD1
|
A:ASN710
|
3.6
|
19.5
|
1.0
|
NH2
|
A:ARG125
|
3.6
|
27.9
|
1.0
|
NE2
|
A:HIS740
|
3.6
|
22.1
|
1.0
|
O20
|
A:0WG800
|
3.7
|
26.0
|
1.0
|
C7
|
A:0WG800
|
3.7
|
29.9
|
1.0
|
N9
|
A:0WG800
|
3.8
|
26.1
|
1.0
|
C19
|
A:0WG800
|
3.8
|
27.6
|
1.0
|
CD2
|
A:HIS740
|
3.8
|
21.6
|
1.0
|
CB
|
A:SER630
|
3.9
|
19.6
|
1.0
|
OH
|
A:TYR662
|
4.0
|
20.9
|
1.0
|
OG
|
A:SER630
|
4.0
|
19.6
|
1.0
|
C14
|
A:0WG800
|
4.1
|
30.1
|
1.0
|
OE1
|
A:GLU205
|
4.2
|
24.0
|
1.0
|
O
|
A:HOH956
|
4.2
|
37.9
|
1.0
|
C12
|
A:0WG800
|
4.2
|
30.9
|
1.0
|
C8
|
A:0WG800
|
4.2
|
28.1
|
1.0
|
CG
|
A:ASN710
|
4.4
|
19.3
|
1.0
|
C3
|
A:0WG800
|
4.4
|
29.9
|
1.0
|
C5
|
A:0WG800
|
4.6
|
30.9
|
1.0
|
C13
|
A:0WG800
|
4.7
|
30.8
|
1.0
|
ND2
|
A:ASN710
|
4.7
|
19.8
|
1.0
|
N21
|
A:0WG800
|
4.8
|
28.0
|
1.0
|
CE1
|
A:HIS740
|
4.8
|
22.4
|
1.0
|
N4
|
A:0WG800
|
4.8
|
30.7
|
1.0
|
CZ
|
A:ARG125
|
4.9
|
28.6
|
1.0
|
|
Bromine binding site 2 out
of 4 in 4g1f
Go back to
Bromine Binding Sites List in 4g1f
Bromine binding site 2 out
of 4 in the Crystal Structure of Human Dipeptidyl Peptidase IV in Complex with A Pyridopyrimidinedione Analogue
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 2 of Crystal Structure of Human Dipeptidyl Peptidase IV in Complex with A Pyridopyrimidinedione Analogue within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Br800
b:46.9
occ:1.00
|
BR1
|
B:0WG800
|
0.0
|
46.9
|
1.0
|
C16
|
B:0WG800
|
1.9
|
36.5
|
1.0
|
C15
|
B:0WG800
|
2.8
|
35.1
|
1.0
|
C11
|
B:0WG800
|
2.9
|
34.5
|
1.0
|
O
|
B:HOH958
|
3.1
|
30.4
|
1.0
|
C10
|
B:0WG800
|
3.1
|
32.2
|
1.0
|
NE2
|
B:HIS740
|
3.5
|
21.7
|
1.0
|
C18
|
B:0WG800
|
3.5
|
32.0
|
1.0
|
N9
|
B:0WG800
|
3.7
|
26.8
|
1.0
|
O20
|
B:0WG800
|
3.7
|
31.9
|
1.0
|
CD2
|
B:HIS740
|
3.7
|
21.6
|
1.0
|
C7
|
B:0WG800
|
3.8
|
30.7
|
1.0
|
NH2
|
B:ARG125
|
3.8
|
30.7
|
1.0
|
OG
|
B:SER630
|
3.8
|
21.6
|
1.0
|
CB
|
B:SER630
|
3.8
|
22.4
|
1.0
|
C19
|
B:0WG800
|
3.8
|
32.0
|
1.0
|
OH
|
B:TYR662
|
4.0
|
27.1
|
1.0
|
OD1
|
B:ASN710
|
4.0
|
20.1
|
1.0
|
C14
|
B:0WG800
|
4.1
|
34.3
|
1.0
|
OE1
|
B:GLU205
|
4.2
|
29.6
|
1.0
|
C12
|
B:0WG800
|
4.2
|
33.8
|
1.0
|
C8
|
B:0WG800
|
4.2
|
28.7
|
1.0
|
ND2
|
B:ASN710
|
4.3
|
21.2
|
1.0
|
CG
|
B:ASN710
|
4.4
|
20.4
|
1.0
|
C3
|
B:0WG800
|
4.5
|
32.1
|
1.0
|
CE1
|
B:HIS740
|
4.5
|
21.8
|
1.0
|
C5
|
B:0WG800
|
4.6
|
31.6
|
1.0
|
C13
|
B:0WG800
|
4.7
|
33.5
|
1.0
|
N21
|
B:0WG800
|
4.8
|
32.7
|
1.0
|
N4
|
B:0WG800
|
4.9
|
32.3
|
1.0
|
CG
|
B:HIS740
|
4.9
|
21.5
|
1.0
|
|
Bromine binding site 3 out
of 4 in 4g1f
Go back to
Bromine Binding Sites List in 4g1f
Bromine binding site 3 out
of 4 in the Crystal Structure of Human Dipeptidyl Peptidase IV in Complex with A Pyridopyrimidinedione Analogue
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 3 of Crystal Structure of Human Dipeptidyl Peptidase IV in Complex with A Pyridopyrimidinedione Analogue within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Br800
b:41.2
occ:1.00
|
BR1
|
C:0WG800
|
0.0
|
41.2
|
1.0
|
C16
|
C:0WG800
|
1.9
|
32.5
|
1.0
|
C15
|
C:0WG800
|
2.8
|
32.1
|
1.0
|
C11
|
C:0WG800
|
2.9
|
31.3
|
1.0
|
C10
|
C:0WG800
|
3.1
|
30.7
|
1.0
|
O
|
C:HOH902
|
3.3
|
13.7
|
1.0
|
NH2
|
C:ARG125
|
3.5
|
27.0
|
1.0
|
NE2
|
C:HIS740
|
3.5
|
25.6
|
1.0
|
C18
|
C:0WG800
|
3.6
|
30.7
|
1.0
|
OD1
|
C:ASN710
|
3.6
|
21.4
|
1.0
|
N9
|
C:0WG800
|
3.7
|
26.5
|
1.0
|
O20
|
C:0WG800
|
3.7
|
31.1
|
1.0
|
C7
|
C:0WG800
|
3.8
|
30.0
|
1.0
|
CD2
|
C:HIS740
|
3.8
|
25.4
|
1.0
|
C19
|
C:0WG800
|
3.9
|
31.2
|
1.0
|
OG
|
C:SER630
|
3.9
|
21.8
|
1.0
|
CB
|
C:SER630
|
4.0
|
21.7
|
1.0
|
OH
|
C:TYR662
|
4.0
|
23.9
|
1.0
|
OE1
|
C:GLU205
|
4.1
|
31.5
|
1.0
|
C14
|
C:0WG800
|
4.2
|
31.4
|
1.0
|
C12
|
C:0WG800
|
4.2
|
30.2
|
1.0
|
C8
|
C:0WG800
|
4.2
|
28.1
|
1.0
|
CG
|
C:ASN710
|
4.4
|
20.9
|
1.0
|
C3
|
C:0WG800
|
4.5
|
30.7
|
1.0
|
CE1
|
C:HIS740
|
4.6
|
25.4
|
1.0
|
C5
|
C:0WG800
|
4.6
|
30.4
|
1.0
|
CZ
|
C:ARG125
|
4.6
|
27.7
|
1.0
|
C13
|
C:0WG800
|
4.7
|
30.5
|
1.0
|
ND2
|
C:ASN710
|
4.7
|
20.2
|
1.0
|
N21
|
C:0WG800
|
4.9
|
31.3
|
1.0
|
N4
|
C:0WG800
|
4.9
|
30.5
|
1.0
|
CG
|
C:HIS740
|
5.0
|
25.5
|
1.0
|
|
Bromine binding site 4 out
of 4 in 4g1f
Go back to
Bromine Binding Sites List in 4g1f
Bromine binding site 4 out
of 4 in the Crystal Structure of Human Dipeptidyl Peptidase IV in Complex with A Pyridopyrimidinedione Analogue
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 4 of Crystal Structure of Human Dipeptidyl Peptidase IV in Complex with A Pyridopyrimidinedione Analogue within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Br800
b:45.5
occ:1.00
|
BR1
|
D:0WG800
|
0.0
|
45.5
|
1.0
|
C16
|
D:0WG800
|
1.9
|
36.4
|
1.0
|
C15
|
D:0WG800
|
2.8
|
34.7
|
1.0
|
C11
|
D:0WG800
|
2.9
|
34.6
|
1.0
|
O
|
D:HOH901
|
3.0
|
15.9
|
1.0
|
C10
|
D:0WG800
|
3.1
|
32.4
|
1.0
|
C18
|
D:0WG800
|
3.6
|
31.5
|
1.0
|
NE2
|
D:HIS740
|
3.6
|
23.8
|
1.0
|
C7
|
D:0WG800
|
3.7
|
31.4
|
1.0
|
NH2
|
D:ARG125
|
3.7
|
24.8
|
1.0
|
O20
|
D:0WG800
|
3.8
|
30.8
|
1.0
|
CD2
|
D:HIS740
|
3.8
|
23.4
|
1.0
|
N9
|
D:0WG800
|
3.8
|
29.6
|
1.0
|
OG
|
D:SER630
|
3.8
|
26.1
|
1.0
|
CB
|
D:SER630
|
3.9
|
26.0
|
1.0
|
C19
|
D:0WG800
|
3.9
|
30.9
|
1.0
|
OH
|
D:TYR662
|
3.9
|
25.3
|
1.0
|
C14
|
D:0WG800
|
4.1
|
34.6
|
1.0
|
OD1
|
D:ASN710
|
4.1
|
25.3
|
1.0
|
C8
|
D:0WG800
|
4.1
|
30.1
|
1.0
|
C12
|
D:0WG800
|
4.2
|
34.5
|
1.0
|
ND2
|
D:ASN710
|
4.2
|
24.7
|
1.0
|
OE1
|
D:GLU205
|
4.3
|
25.0
|
1.0
|
CG
|
D:ASN710
|
4.3
|
24.6
|
1.0
|
C3
|
D:0WG800
|
4.5
|
31.6
|
1.0
|
C5
|
D:0WG800
|
4.6
|
31.5
|
1.0
|
C13
|
D:0WG800
|
4.7
|
35.1
|
1.0
|
CE1
|
D:HIS740
|
4.7
|
23.5
|
1.0
|
CG
|
D:HIS740
|
4.9
|
23.3
|
1.0
|
N4
|
D:0WG800
|
4.9
|
31.8
|
1.0
|
N21
|
D:0WG800
|
4.9
|
30.7
|
1.0
|
CZ
|
D:TYR662
|
4.9
|
25.1
|
1.0
|
CZ
|
D:ARG125
|
5.0
|
25.0
|
1.0
|
|
Reference:
B.Lam,
Z.Zhang,
J.A.Stafford,
R.J.Skene,
L.Shi,
S.L.Gwaltney.
Structure-Based Design of Pyridopyrimidinediones As Dipeptidyl Peptidase IV Inhibitors. Bioorg.Med.Chem.Lett. V. 22 6628 2012.
ISSN: ISSN 0960-894X
PubMed: 23025999
DOI: 10.1016/J.BMCL.2012.08.110
Page generated: Wed Jul 10 21:16:16 2024
|