Fluorine in PDB 6e41: Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and An Epacadostat Analog
Enzymatic activity of Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and An Epacadostat Analog
All present enzymatic activity of Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and An Epacadostat Analog:
1.13.11.52;
Protein crystallography data
The structure of Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and An Epacadostat Analog, PDB code: 6e41
was solved by
S.Luo,
L.Tong,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
55.25 /
2.29
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
80.916,
201.722,
114.893,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
20.3 /
25.1
|
Other elements in 6e41:
The structure of Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and An Epacadostat Analog also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and An Epacadostat Analog
(pdb code 6e41). 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 Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and An Epacadostat Analog, PDB code: 6e41:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 6e41
Go back to
Fluorine Binding Sites List in 6e41
Fluorine binding site 1 out
of 6 in the Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and An Epacadostat Analog
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 Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and An Epacadostat Analog within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F502
b:56.6
occ:1.00
|
F25
|
A:HQS502
|
0.0
|
56.6
|
1.0
|
C21
|
A:HQS502
|
1.4
|
54.6
|
1.0
|
C20
|
A:HQS502
|
2.4
|
46.5
|
1.0
|
C22
|
A:HQS502
|
2.4
|
54.5
|
1.0
|
BR
|
A:HQS502
|
3.1
|
57.8
|
1.0
|
CE1
|
A:PHE164
|
3.3
|
36.0
|
1.0
|
CD1
|
A:PHE164
|
3.3
|
35.0
|
1.0
|
SG
|
A:CYS129
|
3.4
|
38.7
|
1.0
|
C19
|
A:HQS502
|
3.7
|
50.2
|
1.0
|
C23
|
A:HQS502
|
3.7
|
45.6
|
1.0
|
CB
|
A:VAL130
|
4.0
|
40.0
|
1.0
|
CG1
|
A:VAL130
|
4.2
|
47.0
|
1.0
|
C18
|
A:HQS502
|
4.2
|
50.9
|
1.0
|
CD1
|
A:TYR126
|
4.2
|
47.6
|
1.0
|
CE2
|
A:PHE163
|
4.2
|
38.9
|
1.0
|
N
|
A:VAL130
|
4.3
|
38.0
|
1.0
|
C
|
A:CYS129
|
4.5
|
37.1
|
1.0
|
CZ
|
A:PHE164
|
4.5
|
30.2
|
1.0
|
CB
|
A:CYS129
|
4.6
|
33.7
|
1.0
|
CG
|
A:PHE164
|
4.6
|
34.1
|
1.0
|
CD2
|
A:PHE163
|
4.6
|
34.6
|
1.0
|
CA
|
A:VAL130
|
4.7
|
38.4
|
1.0
|
CA
|
A:TYR126
|
4.7
|
37.9
|
1.0
|
CE1
|
A:TYR126
|
4.7
|
39.5
|
1.0
|
O
|
A:CYS129
|
4.8
|
37.1
|
1.0
|
O
|
A:TYR126
|
5.0
|
34.0
|
1.0
|
|
Fluorine binding site 2 out
of 6 in 6e41
Go back to
Fluorine Binding Sites List in 6e41
Fluorine binding site 2 out
of 6 in the Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and An Epacadostat Analog
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 Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and An Epacadostat Analog within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F503
b:49.6
occ:1.00
|
F25
|
A:HQS503
|
0.0
|
49.6
|
1.0
|
C21
|
A:HQS503
|
1.4
|
50.4
|
1.0
|
C22
|
A:HQS503
|
2.4
|
46.0
|
1.0
|
C20
|
A:HQS503
|
2.4
|
43.9
|
1.0
|
BR
|
A:HQS503
|
3.1
|
77.9
|
1.0
|
C23
|
A:HQS503
|
3.7
|
46.5
|
1.0
|
C19
|
A:HQS503
|
3.7
|
46.2
|
1.0
|
CB
|
A:ASN222
|
4.0
|
41.4
|
1.0
|
C18
|
A:HQS503
|
4.2
|
47.9
|
1.0
|
CG
|
A:ASN222
|
4.3
|
42.6
|
1.0
|
ND2
|
A:ASN222
|
4.7
|
50.2
|
1.0
|
OD1
|
A:ASN222
|
4.8
|
51.2
|
1.0
|
CA
|
A:ASN222
|
5.0
|
40.3
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 6e41
Go back to
Fluorine Binding Sites List in 6e41
Fluorine binding site 3 out
of 6 in the Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and An Epacadostat Analog
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 Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and An Epacadostat Analog within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F502
b:53.1
occ:1.00
|
F25
|
B:HQS502
|
0.0
|
53.1
|
1.0
|
C21
|
B:HQS502
|
1.4
|
49.3
|
1.0
|
C22
|
B:HQS502
|
2.4
|
44.7
|
1.0
|
C20
|
B:HQS502
|
2.4
|
45.3
|
1.0
|
CG2
|
B:VAL130
|
2.9
|
34.7
|
1.0
|
BR
|
B:HQS502
|
3.0
|
52.9
|
1.0
|
CD1
|
B:PHE164
|
3.2
|
35.5
|
1.0
|
CE1
|
B:PHE164
|
3.3
|
35.9
|
1.0
|
SG
|
B:CYS129
|
3.5
|
39.5
|
1.0
|
C23
|
B:HQS502
|
3.6
|
40.7
|
1.0
|
C19
|
B:HQS502
|
3.6
|
44.0
|
1.0
|
CE2
|
B:PHE163
|
4.0
|
46.0
|
1.0
|
C18
|
B:HQS502
|
4.1
|
45.0
|
1.0
|
CD2
|
B:PHE163
|
4.3
|
44.8
|
1.0
|
CB
|
B:VAL130
|
4.3
|
40.7
|
1.0
|
CD1
|
B:TYR126
|
4.5
|
34.7
|
1.0
|
CG
|
B:PHE164
|
4.5
|
37.0
|
1.0
|
CZ
|
B:PHE164
|
4.6
|
30.5
|
1.0
|
N
|
B:VAL130
|
4.6
|
36.8
|
1.0
|
C
|
B:CYS129
|
4.7
|
35.7
|
1.0
|
CB
|
B:CYS129
|
4.8
|
34.5
|
1.0
|
O
|
B:CYS129
|
4.8
|
39.3
|
1.0
|
CA
|
B:PHE164
|
4.9
|
32.2
|
1.0
|
CE1
|
B:TYR126
|
4.9
|
36.9
|
1.0
|
CA
|
B:VAL130
|
4.9
|
33.7
|
1.0
|
CZ
|
B:PHE163
|
4.9
|
46.0
|
1.0
|
CD1
|
B:LEU234
|
5.0
|
41.5
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 6e41
Go back to
Fluorine Binding Sites List in 6e41
Fluorine binding site 4 out
of 6 in the Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and An Epacadostat Analog
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 Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and An Epacadostat Analog within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F502
b:58.7
occ:1.00
|
F25
|
C:HQS502
|
0.0
|
58.7
|
1.0
|
C21
|
C:HQS502
|
1.4
|
52.1
|
1.0
|
C22
|
C:HQS502
|
2.4
|
50.1
|
1.0
|
C20
|
C:HQS502
|
2.4
|
50.5
|
1.0
|
CG2
|
C:VAL130
|
2.8
|
42.9
|
1.0
|
BR
|
C:HQS502
|
3.1
|
57.7
|
1.0
|
SG
|
C:CYS129
|
3.3
|
36.3
|
1.0
|
CE1
|
C:PHE164
|
3.4
|
38.7
|
1.0
|
CD1
|
C:PHE164
|
3.5
|
36.1
|
1.0
|
C23
|
C:HQS502
|
3.7
|
44.9
|
1.0
|
C19
|
C:HQS502
|
3.7
|
49.8
|
1.0
|
CE2
|
C:PHE163
|
4.1
|
43.5
|
1.0
|
C18
|
C:HQS502
|
4.2
|
47.5
|
1.0
|
CB
|
C:VAL130
|
4.2
|
45.9
|
1.0
|
CD1
|
C:TYR126
|
4.2
|
43.2
|
1.0
|
N
|
C:VAL130
|
4.4
|
39.5
|
1.0
|
CD2
|
C:PHE163
|
4.5
|
39.9
|
1.0
|
C
|
C:CYS129
|
4.5
|
41.6
|
1.0
|
CB
|
C:CYS129
|
4.6
|
31.7
|
1.0
|
CZ
|
C:PHE164
|
4.6
|
32.4
|
1.0
|
CE1
|
C:TYR126
|
4.7
|
44.5
|
1.0
|
CG
|
C:PHE164
|
4.7
|
37.0
|
1.0
|
CA
|
C:VAL130
|
4.7
|
39.9
|
1.0
|
O
|
C:CYS129
|
4.7
|
37.8
|
1.0
|
CA
|
C:TYR126
|
4.8
|
36.3
|
1.0
|
CD1
|
C:LEU234
|
4.8
|
39.9
|
1.0
|
|
Fluorine binding site 5 out
of 6 in 6e41
Go back to
Fluorine Binding Sites List in 6e41
Fluorine binding site 5 out
of 6 in the Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and An Epacadostat Analog
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 Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and An Epacadostat Analog within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F503
b:54.0
occ:1.00
|
F25
|
C:HQS503
|
0.0
|
54.0
|
1.0
|
C21
|
C:HQS503
|
1.4
|
52.6
|
1.0
|
C22
|
C:HQS503
|
2.4
|
49.5
|
1.0
|
C20
|
C:HQS503
|
2.4
|
49.5
|
1.0
|
BR
|
C:HQS503
|
3.1
|
69.2
|
1.0
|
C23
|
C:HQS503
|
3.7
|
45.7
|
1.0
|
C19
|
C:HQS503
|
3.7
|
50.1
|
1.0
|
CB
|
C:ASN222
|
4.0
|
47.5
|
1.0
|
C18
|
C:HQS503
|
4.2
|
53.0
|
1.0
|
ND2
|
C:ASN222
|
4.4
|
54.2
|
1.0
|
CG
|
C:ASN222
|
4.5
|
52.2
|
1.0
|
|
Fluorine binding site 6 out
of 6 in 6e41
Go back to
Fluorine Binding Sites List in 6e41
Fluorine binding site 6 out
of 6 in the Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and An Epacadostat Analog
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 Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and An Epacadostat Analog within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F502
b:52.1
occ:1.00
|
F25
|
D:HQS502
|
0.0
|
52.1
|
1.0
|
C21
|
D:HQS502
|
1.4
|
53.3
|
1.0
|
C22
|
D:HQS502
|
2.4
|
47.9
|
1.0
|
C20
|
D:HQS502
|
2.4
|
49.1
|
1.0
|
CG2
|
D:VAL130
|
2.8
|
39.4
|
1.0
|
BR
|
D:HQS502
|
3.1
|
52.5
|
1.0
|
CD1
|
D:PHE164
|
3.1
|
37.5
|
1.0
|
CE1
|
D:PHE164
|
3.1
|
36.8
|
1.0
|
SG
|
D:CYS129
|
3.5
|
40.8
|
1.0
|
C23
|
D:HQS502
|
3.7
|
38.8
|
1.0
|
C19
|
D:HQS502
|
3.7
|
43.6
|
1.0
|
CE2
|
D:PHE163
|
4.1
|
43.8
|
1.0
|
C18
|
D:HQS502
|
4.2
|
44.4
|
1.0
|
CB
|
D:VAL130
|
4.2
|
43.7
|
1.0
|
CD2
|
D:PHE163
|
4.4
|
44.0
|
1.0
|
CG
|
D:PHE164
|
4.4
|
36.9
|
1.0
|
CZ
|
D:PHE164
|
4.5
|
36.9
|
1.0
|
CD1
|
D:TYR126
|
4.5
|
38.7
|
1.0
|
N
|
D:VAL130
|
4.5
|
35.4
|
1.0
|
C
|
D:CYS129
|
4.6
|
37.4
|
1.0
|
CB
|
D:CYS129
|
4.7
|
33.4
|
1.0
|
O
|
D:CYS129
|
4.7
|
40.0
|
1.0
|
CA
|
D:VAL130
|
4.8
|
38.0
|
1.0
|
CE1
|
D:TYR126
|
4.9
|
41.2
|
1.0
|
CA
|
D:TYR126
|
4.9
|
32.6
|
1.0
|
CA
|
D:PHE164
|
5.0
|
33.5
|
1.0
|
CD1
|
D:LEU234
|
5.0
|
36.7
|
1.0
|
CZ
|
D:PHE163
|
5.0
|
42.7
|
1.0
|
OG
|
D:SER167
|
5.0
|
35.1
|
1.0
|
|
Reference:
S.Luo,
K.Xu,
S.Xiang,
J.Chen,
C.Chen,
C.Guo,
Y.Tong,
L.Tong.
High-Resolution Structures of Inhibitor Complexes of Human Indoleamine 2,3-Dioxygenase 1 in A New Crystal Form. Acta Crystallogr F Struct V. 74 717 2018BIOL Commun.
ISSN: ESSN 2053-230X
PubMed: 30387777
DOI: 10.1107/S2053230X18012955
Page generated: Thu Aug 1 19:18:55 2024
|