Fluorine in PDB 6pyz: Crystal Structure of Human Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active Site
Enzymatic activity of Crystal Structure of Human Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active Site
All present enzymatic activity of Crystal Structure of Human Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active Site:
1.13.11.11;
Protein crystallography data
The structure of Crystal Structure of Human Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active Site, PDB code: 6pyz
was solved by
K.N.Pham,
A.Lewis-Ballester,
S.R.Yeh,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.86 /
2.02
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
143.648,
154.158,
87.951,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18.9 /
24.3
|
Other elements in 6pyz:
The structure of Crystal Structure of Human Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active Site also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of Human Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active Site
(pdb code 6pyz). 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 Human Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active Site, PDB code: 6pyz:
Jump to Fluorine binding site number:
1;
2;
3;
4;
Fluorine binding site 1 out
of 4 in 6pyz
Go back to
Fluorine Binding Sites List in 6pyz
Fluorine binding site 1 out
of 4 in the Crystal Structure of Human Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active Site
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 Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active Site within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F402
b:79.6
occ:1.00
|
F8
|
A:H7S402
|
0.0
|
79.6
|
1.0
|
CZ3
|
A:H7S402
|
1.4
|
76.7
|
1.0
|
CE3
|
A:H7S402
|
2.3
|
77.2
|
1.0
|
CH2
|
A:H7S402
|
2.4
|
78.2
|
1.0
|
CB
|
A:ALA150
|
2.9
|
55.2
|
1.0
|
CD2
|
B:TYR45
|
3.2
|
43.6
|
1.0
|
CD2
|
A:H7S402
|
3.6
|
82.3
|
1.0
|
CZ2
|
A:H7S402
|
3.6
|
80.0
|
1.0
|
CE2
|
B:TYR45
|
3.7
|
46.0
|
1.0
|
CG
|
B:TYR45
|
3.8
|
45.4
|
1.0
|
C
|
A:ALA150
|
3.9
|
58.6
|
1.0
|
CD2
|
A:LEU147
|
3.9
|
62.5
|
1.0
|
O
|
A:ALA150
|
4.0
|
56.5
|
1.0
|
CA
|
A:ALA150
|
4.0
|
56.3
|
1.0
|
CE2
|
A:H7S402
|
4.1
|
80.0
|
1.0
|
CB
|
B:TYR45
|
4.1
|
41.2
|
1.0
|
O
|
A:LEU147
|
4.2
|
51.1
|
1.0
|
CB
|
A:LEU147
|
4.3
|
62.5
|
1.0
|
N
|
A:SER151
|
4.3
|
57.7
|
1.0
|
CA
|
B:TYR42
|
4.4
|
41.9
|
1.0
|
CD2
|
B:LEU40
|
4.6
|
65.8
|
1.0
|
CG
|
A:LEU147
|
4.6
|
62.9
|
1.0
|
CZ
|
B:TYR45
|
4.6
|
46.9
|
1.0
|
CA
|
A:LEU147
|
4.7
|
59.9
|
1.0
|
CD1
|
B:TYR45
|
4.7
|
47.3
|
1.0
|
C
|
A:LEU147
|
4.8
|
57.2
|
1.0
|
CD2
|
B:TYR42
|
4.9
|
39.1
|
1.0
|
CE2
|
A:PHE72
|
4.9
|
37.0
|
1.0
|
CG
|
A:H7S402
|
4.9
|
83.2
|
1.0
|
N
|
B:TYR42
|
4.9
|
46.2
|
1.0
|
N
|
A:ALA150
|
5.0
|
64.3
|
1.0
|
|
Fluorine binding site 2 out
of 4 in 6pyz
Go back to
Fluorine Binding Sites List in 6pyz
Fluorine binding site 2 out
of 4 in the Crystal Structure of Human Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active Site
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 Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active Site within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F402
b:74.4
occ:1.00
|
F8
|
B:H7S402
|
0.0
|
74.4
|
1.0
|
CZ3
|
B:H7S402
|
1.4
|
68.8
|
1.0
|
CE3
|
B:H7S402
|
2.3
|
68.2
|
1.0
|
CH2
|
B:H7S402
|
2.4
|
66.6
|
1.0
|
CB
|
B:ALA150
|
3.1
|
53.9
|
1.0
|
CD2
|
A:TYR45
|
3.2
|
38.5
|
1.0
|
CG
|
A:TYR45
|
3.5
|
40.0
|
1.0
|
CD2
|
B:H7S402
|
3.6
|
69.7
|
1.0
|
CZ2
|
B:H7S402
|
3.6
|
68.0
|
1.0
|
CB
|
A:TYR45
|
3.7
|
40.5
|
1.0
|
CE2
|
A:TYR45
|
3.8
|
41.8
|
1.0
|
CD2
|
B:LEU147
|
4.1
|
59.6
|
1.0
|
CE2
|
B:H7S402
|
4.1
|
70.5
|
1.0
|
CA
|
B:ALA150
|
4.2
|
56.4
|
1.0
|
C
|
B:ALA150
|
4.2
|
57.0
|
1.0
|
CA
|
A:TYR42
|
4.3
|
41.7
|
1.0
|
O
|
B:LEU147
|
4.4
|
54.9
|
1.0
|
CD1
|
A:TYR45
|
4.4
|
41.6
|
1.0
|
N
|
B:SER151
|
4.5
|
57.4
|
1.0
|
O
|
B:ALA150
|
4.6
|
58.3
|
1.0
|
CB
|
B:LEU147
|
4.6
|
58.2
|
1.0
|
CD2
|
A:LEU40
|
4.7
|
65.5
|
1.0
|
CZ
|
A:TYR45
|
4.7
|
41.0
|
1.0
|
CD1
|
A:TYR42
|
4.7
|
37.7
|
1.0
|
N
|
A:TYR42
|
4.8
|
44.0
|
1.0
|
CG
|
B:LEU147
|
4.9
|
58.0
|
1.0
|
CA
|
B:LEU147
|
4.9
|
56.5
|
1.0
|
O
|
A:TYR42
|
4.9
|
36.8
|
1.0
|
CG
|
B:H7S402
|
5.0
|
67.3
|
1.0
|
CE2
|
B:PHE72
|
5.0
|
37.5
|
1.0
|
CE1
|
A:TYR45
|
5.0
|
42.9
|
1.0
|
CB
|
A:TYR42
|
5.0
|
41.7
|
1.0
|
|
Fluorine binding site 3 out
of 4 in 6pyz
Go back to
Fluorine Binding Sites List in 6pyz
Fluorine binding site 3 out
of 4 in the Crystal Structure of Human Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active Site
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 Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active Site within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F402
b:78.1
occ:1.00
|
F8
|
C:H7S402
|
0.0
|
78.1
|
1.0
|
CZ3
|
C:H7S402
|
1.4
|
75.0
|
1.0
|
CH2
|
C:H7S402
|
2.3
|
71.8
|
1.0
|
CE3
|
C:H7S402
|
2.3
|
77.0
|
1.0
|
CB
|
C:ALA150
|
3.0
|
62.2
|
1.0
|
CD2
|
D:TYR45
|
3.3
|
45.8
|
1.0
|
CZ2
|
C:H7S402
|
3.6
|
73.8
|
1.0
|
CD2
|
C:H7S402
|
3.6
|
78.7
|
1.0
|
CG
|
D:TYR45
|
3.7
|
46.8
|
1.0
|
CE2
|
D:TYR45
|
3.8
|
49.3
|
1.0
|
CB
|
D:TYR45
|
4.0
|
43.4
|
1.0
|
CE2
|
C:H7S402
|
4.1
|
79.7
|
1.0
|
C
|
C:ALA150
|
4.1
|
67.6
|
1.0
|
CA
|
C:ALA150
|
4.2
|
62.2
|
1.0
|
CD2
|
C:LEU147
|
4.2
|
59.9
|
1.0
|
O
|
C:ALA150
|
4.3
|
68.8
|
1.0
|
CA
|
D:TYR42
|
4.3
|
48.6
|
1.0
|
O
|
C:LEU147
|
4.3
|
56.0
|
1.0
|
CB
|
C:LEU147
|
4.4
|
60.6
|
1.0
|
N
|
C:SER151
|
4.5
|
68.2
|
1.0
|
CD1
|
D:TYR45
|
4.6
|
47.2
|
1.0
|
N
|
D:TYR42
|
4.7
|
48.3
|
1.0
|
CZ
|
D:TYR45
|
4.7
|
48.7
|
1.0
|
CG
|
C:LEU147
|
4.7
|
59.2
|
1.0
|
CD1
|
D:TYR42
|
4.8
|
50.3
|
1.0
|
CA
|
C:LEU147
|
4.8
|
58.4
|
1.0
|
CE2
|
C:PHE72
|
4.9
|
41.0
|
1.0
|
CG
|
C:H7S402
|
5.0
|
82.8
|
1.0
|
CD2
|
D:LEU40
|
5.0
|
68.2
|
1.0
|
CD1
|
C:LEU147
|
5.0
|
59.0
|
1.0
|
O
|
D:TYR42
|
5.0
|
42.8
|
1.0
|
CB
|
D:TYR42
|
5.0
|
50.2
|
1.0
|
|
Fluorine binding site 4 out
of 4 in 6pyz
Go back to
Fluorine Binding Sites List in 6pyz
Fluorine binding site 4 out
of 4 in the Crystal Structure of Human Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active Site
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 Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active Site within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F402
b:70.0
occ:1.00
|
F8
|
D:H7S402
|
0.0
|
70.0
|
1.0
|
CZ3
|
D:H7S402
|
1.4
|
66.7
|
1.0
|
CE3
|
D:H7S402
|
2.3
|
62.6
|
1.0
|
CH2
|
D:H7S402
|
2.4
|
61.1
|
1.0
|
CB
|
D:ALA150
|
3.1
|
50.5
|
1.0
|
CD2
|
C:TYR45
|
3.2
|
35.8
|
1.0
|
CG
|
C:TYR45
|
3.5
|
40.4
|
1.0
|
CD2
|
D:H7S402
|
3.6
|
66.1
|
1.0
|
CZ2
|
D:H7S402
|
3.6
|
61.1
|
1.0
|
CE2
|
C:TYR45
|
3.7
|
38.8
|
1.0
|
CB
|
C:TYR45
|
3.9
|
40.9
|
1.0
|
CE2
|
D:H7S402
|
4.1
|
66.3
|
1.0
|
CD2
|
D:LEU147
|
4.1
|
51.5
|
1.0
|
CB
|
D:LEU147
|
4.2
|
50.8
|
1.0
|
O
|
D:LEU147
|
4.3
|
51.4
|
1.0
|
CD1
|
C:TYR45
|
4.3
|
42.0
|
1.0
|
CA
|
D:ALA150
|
4.3
|
52.4
|
1.0
|
C
|
D:ALA150
|
4.3
|
53.3
|
1.0
|
CA
|
C:TYR42
|
4.4
|
43.7
|
1.0
|
CZ
|
C:TYR45
|
4.5
|
38.0
|
1.0
|
O
|
D:ALA150
|
4.5
|
51.3
|
1.0
|
CD2
|
C:LEU40
|
4.5
|
65.7
|
1.0
|
CG
|
D:LEU147
|
4.6
|
50.0
|
1.0
|
CA
|
D:LEU147
|
4.6
|
51.2
|
1.0
|
CE1
|
C:TYR45
|
4.7
|
37.5
|
1.0
|
N
|
D:SER151
|
4.8
|
51.7
|
1.0
|
N
|
C:TYR42
|
4.8
|
45.7
|
1.0
|
CE2
|
D:PHE72
|
4.8
|
40.9
|
1.0
|
CD1
|
D:LEU147
|
4.9
|
52.3
|
1.0
|
C
|
D:LEU147
|
4.9
|
50.9
|
1.0
|
CG
|
D:H7S402
|
4.9
|
68.5
|
1.0
|
CD1
|
C:TYR42
|
5.0
|
43.5
|
1.0
|
|
Reference:
K.N.Pham,
A.Lewis-Ballester,
S.R.Yeh.
Structural Basis of Inhibitor Selectivity in Human Indoleamine 2,3-Dioxygenase 1 and Tryptophan Dioxygenase. J.Am.Chem.Soc. V. 141 18771 2019.
ISSN: ESSN 1520-5126
PubMed: 31682426
DOI: 10.1021/JACS.9B08871
Page generated: Fri Aug 2 00:32:29 2024
|