Fluorine in PDB 7rrc: IDO1 in Complex with Compound 14
Enzymatic activity of IDO1 in Complex with Compound 14
All present enzymatic activity of IDO1 in Complex with Compound 14:
1.13.11.52;
Protein crystallography data
The structure of IDO1 in Complex with Compound 14, PDB code: 7rrc
was solved by
C.A.Lesburg,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
74.59 /
2.18
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
84.95,
91.339,
129.223,
90,
90,
90
|
R / Rfree (%)
|
18.7 /
21.7
|
Fluorine Binding Sites:
The binding sites of Fluorine atom in the IDO1 in Complex with Compound 14
(pdb code 7rrc). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the
IDO1 in Complex with Compound 14, PDB code: 7rrc:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Fluorine binding site 1 out
of 8 in 7rrc
Go back to
Fluorine Binding Sites List in 7rrc
Fluorine binding site 1 out
of 8 in the IDO1 in Complex with Compound 14
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of IDO1 in Complex with Compound 14 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F501
b:47.3
occ:1.00
|
F8
|
A:6RI501
|
0.0
|
47.3
|
1.0
|
C7
|
A:6RI501
|
1.3
|
40.7
|
1.0
|
C9
|
A:6RI501
|
2.3
|
45.4
|
1.0
|
C6
|
A:6RI501
|
2.4
|
41.3
|
1.0
|
CA
|
A:GLY262
|
3.4
|
49.8
|
1.0
|
SG
|
A:CYS129
|
3.5
|
45.4
|
1.0
|
C10
|
A:6RI501
|
3.6
|
47.0
|
1.0
|
C
|
A:GLY262
|
3.6
|
49.6
|
1.0
|
C5
|
A:6RI501
|
3.6
|
39.1
|
1.0
|
N
|
A:SER263
|
3.8
|
48.7
|
1.0
|
CD2
|
A:LEU234
|
4.1
|
49.8
|
1.0
|
C4
|
A:6RI501
|
4.1
|
41.3
|
1.0
|
CD1
|
A:LEU234
|
4.2
|
45.3
|
1.0
|
O
|
A:GLY262
|
4.2
|
46.9
|
1.0
|
CA
|
A:TYR126
|
4.3
|
41.5
|
1.0
|
CD2
|
A:TYR126
|
4.4
|
41.1
|
1.0
|
N
|
A:TYR126
|
4.5
|
43.5
|
1.0
|
CG
|
A:LEU234
|
4.6
|
43.0
|
1.0
|
CB
|
A:TYR126
|
4.6
|
40.9
|
1.0
|
N
|
A:GLY262
|
4.7
|
44.6
|
1.0
|
CA
|
A:SER263
|
4.7
|
50.5
|
1.0
|
CB
|
A:LEU234
|
4.8
|
46.8
|
1.0
|
OE1
|
A:GLN266
|
4.9
|
41.5
|
1.0
|
CE1
|
A:PHE164
|
4.9
|
51.0
|
1.0
|
C
|
A:SER263
|
4.9
|
49.6
|
1.0
|
C
|
A:VAL125
|
5.0
|
46.5
|
1.0
|
|
Fluorine binding site 2 out
of 8 in 7rrc
Go back to
Fluorine Binding Sites List in 7rrc
Fluorine binding site 2 out
of 8 in the IDO1 in Complex with Compound 14
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of IDO1 in Complex with Compound 14 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F501
b:54.8
occ:1.00
|
F30
|
A:6RI501
|
0.0
|
54.8
|
1.0
|
C29
|
A:6RI501
|
1.4
|
53.5
|
1.0
|
F31
|
A:6RI501
|
2.2
|
55.4
|
1.0
|
F32
|
A:6RI501
|
2.3
|
57.7
|
1.0
|
C24
|
A:6RI501
|
2.4
|
55.9
|
1.0
|
N23
|
A:6RI501
|
2.7
|
63.6
|
1.0
|
CB
|
A:LEU342
|
3.2
|
40.9
|
1.0
|
CD1
|
A:LEU342
|
3.6
|
45.8
|
1.0
|
CZ
|
A:ARG343
|
3.7
|
66.4
|
1.0
|
C25
|
A:6RI501
|
3.7
|
48.4
|
1.0
|
NH1
|
A:ARG343
|
3.7
|
69.8
|
1.0
|
CD2
|
A:LEU339
|
3.7
|
51.0
|
1.0
|
NE
|
A:ARG343
|
3.8
|
56.4
|
1.0
|
CG
|
A:LEU342
|
3.9
|
41.8
|
1.0
|
C22
|
A:6RI501
|
4.0
|
61.0
|
1.0
|
NH2
|
A:ARG343
|
4.1
|
61.1
|
1.0
|
CD
|
A:ARG343
|
4.1
|
57.3
|
1.0
|
O
|
A:LEU339
|
4.3
|
41.7
|
1.0
|
CA
|
A:LEU342
|
4.5
|
43.8
|
1.0
|
C
|
A:LEU342
|
4.6
|
41.8
|
1.0
|
CD2
|
A:LEU342
|
4.6
|
49.4
|
1.0
|
N
|
A:ARG343
|
4.6
|
43.5
|
1.0
|
CA
|
A:LEU339
|
4.7
|
43.8
|
1.0
|
C26
|
A:6RI501
|
4.8
|
56.9
|
1.0
|
CG
|
A:ARG343
|
4.9
|
52.2
|
1.0
|
CB
|
A:LEU339
|
4.9
|
45.2
|
1.0
|
C21
|
A:6RI501
|
4.9
|
53.1
|
1.0
|
CG
|
A:LEU339
|
5.0
|
50.3
|
1.0
|
|
Fluorine binding site 3 out
of 8 in 7rrc
Go back to
Fluorine Binding Sites List in 7rrc
Fluorine binding site 3 out
of 8 in the IDO1 in Complex with Compound 14
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of IDO1 in Complex with Compound 14 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F501
b:55.4
occ:1.00
|
F31
|
A:6RI501
|
0.0
|
55.4
|
1.0
|
C29
|
A:6RI501
|
1.4
|
53.5
|
1.0
|
F30
|
A:6RI501
|
2.2
|
54.8
|
1.0
|
F32
|
A:6RI501
|
2.3
|
57.7
|
1.0
|
C24
|
A:6RI501
|
2.4
|
55.9
|
1.0
|
C25
|
A:6RI501
|
3.0
|
48.4
|
1.0
|
NH2
|
A:ARG343
|
3.2
|
61.1
|
1.0
|
NH1
|
A:ARG343
|
3.2
|
69.8
|
1.0
|
O
|
A:VAL269
|
3.2
|
50.2
|
1.0
|
CZ
|
A:ARG343
|
3.3
|
66.4
|
1.0
|
N23
|
A:6RI501
|
3.4
|
63.6
|
1.0
|
CA
|
A:PHE270
|
3.4
|
48.1
|
1.0
|
O
|
A:HOH621
|
3.6
|
43.4
|
1.0
|
O
|
A:PHE270
|
3.8
|
50.0
|
1.0
|
C
|
A:VAL269
|
3.9
|
44.6
|
1.0
|
C
|
A:PHE270
|
3.9
|
47.5
|
1.0
|
N
|
A:PHE270
|
3.9
|
47.4
|
1.0
|
NE
|
A:ARG343
|
4.2
|
56.4
|
1.0
|
CD2
|
A:LEU339
|
4.2
|
51.0
|
1.0
|
C26
|
A:6RI501
|
4.3
|
56.9
|
1.0
|
CB
|
A:PHE270
|
4.4
|
45.3
|
1.0
|
C22
|
A:6RI501
|
4.5
|
61.0
|
1.0
|
CG
|
A:PHE270
|
4.5
|
45.7
|
1.0
|
CG1
|
A:VAL269
|
4.5
|
51.0
|
1.0
|
CD2
|
A:PHE270
|
4.6
|
49.9
|
1.0
|
OD1
|
A:ASP274
|
4.7
|
63.4
|
1.0
|
C21
|
A:6RI501
|
4.9
|
53.1
|
1.0
|
N
|
A:GLN271
|
4.9
|
45.5
|
1.0
|
CD
|
A:ARG343
|
5.0
|
57.3
|
1.0
|
|
Fluorine binding site 4 out
of 8 in 7rrc
Go back to
Fluorine Binding Sites List in 7rrc
Fluorine binding site 4 out
of 8 in the IDO1 in Complex with Compound 14
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of IDO1 in Complex with Compound 14 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F501
b:57.7
occ:1.00
|
F32
|
A:6RI501
|
0.0
|
57.7
|
1.0
|
C29
|
A:6RI501
|
1.4
|
53.5
|
1.0
|
F31
|
A:6RI501
|
2.3
|
55.4
|
1.0
|
F30
|
A:6RI501
|
2.3
|
54.8
|
1.0
|
C24
|
A:6RI501
|
2.4
|
55.9
|
1.0
|
C25
|
A:6RI501
|
2.9
|
48.4
|
1.0
|
N23
|
A:6RI501
|
3.4
|
63.6
|
1.0
|
CG1
|
A:VAL269
|
3.6
|
51.0
|
1.0
|
CD1
|
A:LEU342
|
3.7
|
45.8
|
1.0
|
O
|
A:VAL269
|
3.9
|
50.2
|
1.0
|
CD2
|
A:LEU339
|
4.0
|
51.0
|
1.0
|
C26
|
A:6RI501
|
4.2
|
56.9
|
1.0
|
CD2
|
A:LEU207
|
4.5
|
47.0
|
1.0
|
C
|
A:VAL269
|
4.5
|
44.6
|
1.0
|
C22
|
A:6RI501
|
4.6
|
61.0
|
1.0
|
CG
|
A:LEU342
|
4.6
|
41.8
|
1.0
|
CB
|
A:LEU342
|
4.6
|
40.9
|
1.0
|
CB
|
A:VAL269
|
4.9
|
50.1
|
1.0
|
O
|
A:HOH621
|
4.9
|
43.4
|
1.0
|
CD2
|
A:LEU342
|
4.9
|
49.4
|
1.0
|
CD2
|
A:PHE273
|
4.9
|
49.0
|
1.0
|
C21
|
A:6RI501
|
4.9
|
53.1
|
1.0
|
N
|
A:PHE270
|
5.0
|
47.4
|
1.0
|
|
Fluorine binding site 5 out
of 8 in 7rrc
Go back to
Fluorine Binding Sites List in 7rrc
Fluorine binding site 5 out
of 8 in the IDO1 in Complex with Compound 14
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of IDO1 in Complex with Compound 14 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F501
b:46.5
occ:1.00
|
F8
|
B:6RI501
|
0.0
|
46.5
|
1.0
|
C7
|
B:6RI501
|
1.3
|
48.7
|
1.0
|
C6
|
B:6RI501
|
2.3
|
46.0
|
1.0
|
C9
|
B:6RI501
|
2.4
|
46.6
|
1.0
|
SG
|
B:CYS129
|
3.4
|
43.3
|
1.0
|
CA
|
B:GLY262
|
3.6
|
46.2
|
1.0
|
C5
|
B:6RI501
|
3.6
|
38.1
|
1.0
|
C10
|
B:6RI501
|
3.6
|
46.5
|
1.0
|
C
|
B:GLY262
|
3.7
|
48.3
|
1.0
|
N
|
B:SER263
|
3.9
|
42.9
|
1.0
|
CD2
|
B:LEU234
|
4.0
|
49.0
|
1.0
|
C4
|
B:6RI501
|
4.1
|
46.9
|
1.0
|
CD1
|
B:LEU234
|
4.1
|
42.1
|
1.0
|
O
|
B:GLY262
|
4.3
|
44.5
|
1.0
|
CA
|
B:TYR126
|
4.3
|
37.9
|
1.0
|
CD2
|
B:TYR126
|
4.5
|
43.5
|
1.0
|
N
|
B:TYR126
|
4.5
|
44.5
|
1.0
|
CG
|
B:LEU234
|
4.6
|
48.5
|
1.0
|
CB
|
B:TYR126
|
4.7
|
41.7
|
1.0
|
CE1
|
B:PHE164
|
4.7
|
40.2
|
1.0
|
CA
|
B:SER263
|
4.8
|
47.5
|
1.0
|
N
|
B:GLY262
|
4.8
|
41.2
|
1.0
|
O
|
B:SER263
|
4.9
|
41.9
|
1.0
|
OE1
|
B:GLN266
|
4.9
|
39.0
|
1.0
|
C
|
B:SER263
|
4.9
|
46.4
|
1.0
|
C
|
B:VAL125
|
5.0
|
41.3
|
1.0
|
|
Fluorine binding site 6 out
of 8 in 7rrc
Go back to
Fluorine Binding Sites List in 7rrc
Fluorine binding site 6 out
of 8 in the IDO1 in Complex with Compound 14
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of IDO1 in Complex with Compound 14 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F501
b:53.7
occ:1.00
|
F30
|
B:6RI501
|
0.0
|
53.7
|
1.0
|
C29
|
B:6RI501
|
1.4
|
62.6
|
1.0
|
F31
|
B:6RI501
|
2.2
|
62.1
|
1.0
|
F32
|
B:6RI501
|
2.4
|
59.2
|
1.0
|
C24
|
B:6RI501
|
2.4
|
54.0
|
1.0
|
N23
|
B:6RI501
|
2.6
|
62.2
|
1.0
|
CB
|
B:LEU342
|
3.3
|
45.3
|
1.0
|
CD2
|
B:LEU339
|
3.6
|
49.1
|
1.0
|
NH1
|
B:ARG343
|
3.7
|
80.9
|
1.0
|
CD1
|
B:LEU342
|
3.7
|
46.9
|
1.0
|
C25
|
B:6RI501
|
3.7
|
53.5
|
1.0
|
CZ
|
B:ARG343
|
3.7
|
58.1
|
1.0
|
NE
|
B:ARG343
|
3.8
|
60.6
|
1.0
|
C22
|
B:6RI501
|
3.9
|
60.1
|
1.0
|
CD
|
B:ARG343
|
4.0
|
49.3
|
1.0
|
CG
|
B:LEU342
|
4.0
|
47.0
|
1.0
|
O
|
B:LEU339
|
4.3
|
41.8
|
1.0
|
NH2
|
B:ARG343
|
4.3
|
60.9
|
1.0
|
CA
|
B:LEU342
|
4.5
|
41.4
|
1.0
|
C
|
B:LEU342
|
4.6
|
46.9
|
1.0
|
CD2
|
B:LEU342
|
4.6
|
46.9
|
1.0
|
N
|
B:ARG343
|
4.6
|
48.7
|
1.0
|
CA
|
B:LEU339
|
4.7
|
46.7
|
1.0
|
C26
|
B:6RI501
|
4.8
|
61.0
|
1.0
|
CG
|
B:LEU339
|
4.8
|
47.1
|
1.0
|
C21
|
B:6RI501
|
4.9
|
52.8
|
1.0
|
CB
|
B:LEU339
|
4.9
|
48.6
|
1.0
|
CG
|
B:ARG343
|
5.0
|
49.3
|
1.0
|
C
|
B:LEU339
|
5.0
|
43.4
|
1.0
|
|
Fluorine binding site 7 out
of 8 in 7rrc
Go back to
Fluorine Binding Sites List in 7rrc
Fluorine binding site 7 out
of 8 in the IDO1 in Complex with Compound 14
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 7 of IDO1 in Complex with Compound 14 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F501
b:62.1
occ:1.00
|
F31
|
B:6RI501
|
0.0
|
62.1
|
1.0
|
C29
|
B:6RI501
|
1.4
|
62.6
|
1.0
|
F30
|
B:6RI501
|
2.2
|
53.7
|
1.0
|
F32
|
B:6RI501
|
2.3
|
59.2
|
1.0
|
C24
|
B:6RI501
|
2.4
|
54.0
|
1.0
|
C25
|
B:6RI501
|
3.0
|
53.5
|
1.0
|
N23
|
B:6RI501
|
3.3
|
62.2
|
1.0
|
CA
|
B:PHE270
|
3.3
|
51.1
|
1.0
|
O
|
B:VAL269
|
3.4
|
54.0
|
1.0
|
NH1
|
B:ARG343
|
3.4
|
80.9
|
1.0
|
CZ
|
B:ARG343
|
3.6
|
58.1
|
1.0
|
O
|
B:PHE270
|
3.6
|
54.7
|
1.0
|
NH2
|
B:ARG343
|
3.7
|
60.9
|
1.0
|
C
|
B:PHE270
|
3.8
|
51.8
|
1.0
|
O
|
B:HOH672
|
3.8
|
55.8
|
1.0
|
N
|
B:PHE270
|
3.9
|
48.5
|
1.0
|
C
|
B:VAL269
|
3.9
|
51.5
|
1.0
|
CD2
|
B:LEU339
|
4.0
|
49.1
|
1.0
|
C26
|
B:6RI501
|
4.3
|
61.0
|
1.0
|
NE
|
B:ARG343
|
4.4
|
60.6
|
1.0
|
C22
|
B:6RI501
|
4.4
|
60.1
|
1.0
|
CB
|
B:PHE270
|
4.5
|
55.8
|
1.0
|
CG1
|
B:VAL269
|
4.5
|
49.9
|
1.0
|
CG
|
B:PHE270
|
4.6
|
48.3
|
1.0
|
CD2
|
B:PHE270
|
4.6
|
61.2
|
1.0
|
C21
|
B:6RI501
|
4.9
|
52.8
|
1.0
|
N
|
B:GLN271
|
4.9
|
49.2
|
1.0
|
OD2
|
B:ASP274
|
4.9
|
64.9
|
1.0
|
|
Fluorine binding site 8 out
of 8 in 7rrc
Go back to
Fluorine Binding Sites List in 7rrc
Fluorine binding site 8 out
of 8 in the IDO1 in Complex with Compound 14
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 8 of IDO1 in Complex with Compound 14 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F501
b:59.2
occ:1.00
|
F32
|
B:6RI501
|
0.0
|
59.2
|
1.0
|
C29
|
B:6RI501
|
1.4
|
62.6
|
1.0
|
F31
|
B:6RI501
|
2.3
|
62.1
|
1.0
|
F30
|
B:6RI501
|
2.4
|
53.7
|
1.0
|
C24
|
B:6RI501
|
2.4
|
54.0
|
1.0
|
C25
|
B:6RI501
|
2.9
|
53.5
|
1.0
|
N23
|
B:6RI501
|
3.4
|
62.2
|
1.0
|
CD1
|
B:LEU342
|
3.5
|
46.9
|
1.0
|
CG1
|
B:VAL269
|
3.7
|
49.9
|
1.0
|
CD2
|
B:LEU339
|
3.9
|
49.1
|
1.0
|
O
|
B:VAL269
|
4.2
|
54.0
|
1.0
|
C26
|
B:6RI501
|
4.2
|
61.0
|
1.0
|
CG
|
B:LEU342
|
4.4
|
47.0
|
1.0
|
CD2
|
B:LEU207
|
4.4
|
52.7
|
1.0
|
CB
|
B:LEU342
|
4.5
|
45.3
|
1.0
|
C22
|
B:6RI501
|
4.5
|
60.1
|
1.0
|
CD2
|
B:LEU342
|
4.6
|
46.9
|
1.0
|
C
|
B:VAL269
|
4.7
|
51.5
|
1.0
|
C21
|
B:6RI501
|
4.9
|
52.8
|
1.0
|
CD2
|
B:PHE273
|
4.9
|
51.0
|
1.0
|
CB
|
B:VAL269
|
5.0
|
51.0
|
1.0
|
|
Reference:
D.Li,
D.L.Sloman,
A.Achab,
H.Zhou,
M.A.Mcgowan,
C.White,
C.Gibeau,
H.Zhang,
Q.Pu,
I.Bharathan,
B.Hopkins,
K.Liu,
H.Ferguson,
X.Fradera,
C.A.Lesburg,
T.A.Martinot,
J.Qi,
Z.J.Song,
J.Yin,
H.Zhang,
L.Song,
B.Wan,
S.Daddio,
N.Solban,
J.R.Miller,
B.Zamlynny,
A.Bass,
E.Freeland,
B.Ykoruk,
C.Hilliard,
J.Ferraro,
J.Zhai,
I.Knemeyer,
K.M.Otte,
S.Vincent,
N.Sciammetta,
A.Pasternak,
D.J.Bennett,
Y.Han.
Oxetane Promise Delivered: Discovery of Long-Acting IDO1 Inhibitors Suitable For Q3W Oral or Parenteral Dosing. J.Med.Chem. V. 65 6001 2022.
ISSN: ISSN 0022-2623
PubMed: 35239336
DOI: 10.1021/ACS.JMEDCHEM.1C01670
Page generated: Fri Aug 2 12:21:21 2024
|