Fluorine in PDB 7m0m: HPK1 in Complex with Compound 1
Enzymatic activity of HPK1 in Complex with Compound 1
All present enzymatic activity of HPK1 in Complex with Compound 1:
2.7.11.1;
Protein crystallography data
The structure of HPK1 in Complex with Compound 1, PDB code: 7m0m
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)
|
63.31 /
1.93
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
51.168,
56.994,
63.459,
86.73,
86.63,
67.06
|
R / Rfree (%)
|
18.6 /
22
|
Fluorine Binding Sites:
The binding sites of Fluorine atom in the HPK1 in Complex with Compound 1
(pdb code 7m0m). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the
HPK1 in Complex with Compound 1, PDB code: 7m0m:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Fluorine binding site 1 out
of 8 in 7m0m
Go back to
Fluorine Binding Sites List in 7m0m
Fluorine binding site 1 out
of 8 in the HPK1 in Complex with Compound 1
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of HPK1 in Complex with Compound 1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F301
b:31.1
occ:1.00
|
F17
|
A:YK1301
|
0.0
|
31.1
|
1.0
|
C16
|
A:YK1301
|
1.3
|
32.2
|
1.0
|
C15
|
A:YK1301
|
2.3
|
35.6
|
1.0
|
C11
|
A:YK1301
|
2.4
|
33.9
|
1.0
|
N3
|
A:YK1301
|
2.7
|
24.2
|
1.0
|
N10
|
A:YK1301
|
2.8
|
31.9
|
1.0
|
C4
|
A:YK1301
|
3.0
|
28.3
|
1.0
|
CB
|
A:VAL31
|
3.0
|
33.9
|
1.0
|
CG1
|
A:VAL31
|
3.1
|
32.4
|
1.0
|
CB
|
A:LEU23
|
3.3
|
37.7
|
1.0
|
CD1
|
A:LEU23
|
3.5
|
38.1
|
1.0
|
CG2
|
A:VAL31
|
3.5
|
36.1
|
1.0
|
C14
|
A:YK1301
|
3.6
|
33.8
|
1.0
|
C12
|
A:YK1301
|
3.6
|
32.8
|
1.0
|
C24
|
A:YK1301
|
3.7
|
29.7
|
1.0
|
C2
|
A:YK1301
|
3.7
|
24.3
|
1.0
|
CG
|
A:LEU23
|
4.0
|
36.1
|
1.0
|
C13
|
A:YK1301
|
4.1
|
32.7
|
1.0
|
C5
|
A:YK1301
|
4.1
|
27.6
|
1.0
|
C23
|
A:YK1301
|
4.2
|
27.4
|
1.0
|
N22
|
A:YK1301
|
4.3
|
26.0
|
1.0
|
CA
|
A:VAL31
|
4.4
|
35.3
|
1.0
|
C25
|
A:YK1301
|
4.5
|
26.6
|
1.0
|
CA
|
A:LEU23
|
4.5
|
42.3
|
1.0
|
C
|
A:LEU23
|
4.6
|
44.7
|
1.0
|
N1
|
A:YK1301
|
4.6
|
22.7
|
1.0
|
O
|
A:VAL31
|
4.6
|
34.8
|
1.0
|
C34
|
A:YK1301
|
4.7
|
28.2
|
1.0
|
C
|
A:VAL31
|
4.7
|
34.4
|
1.0
|
O
|
A:GLY24
|
4.7
|
46.5
|
1.0
|
O
|
A:LEU23
|
4.8
|
55.2
|
1.0
|
C6
|
A:YK1301
|
4.8
|
24.8
|
1.0
|
N
|
A:GLY24
|
4.9
|
45.1
|
1.0
|
C18
|
A:YK1301
|
4.9
|
36.8
|
1.0
|
|
Fluorine binding site 2 out
of 8 in 7m0m
Go back to
Fluorine Binding Sites List in 7m0m
Fluorine binding site 2 out
of 8 in the HPK1 in Complex with Compound 1
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of HPK1 in Complex with Compound 1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F301
b:37.7
occ:1.00
|
F19
|
A:YK1301
|
0.0
|
37.7
|
1.0
|
C18
|
A:YK1301
|
1.4
|
36.8
|
1.0
|
F21
|
A:YK1301
|
2.2
|
34.5
|
1.0
|
F20
|
A:YK1301
|
2.3
|
41.2
|
1.0
|
C12
|
A:YK1301
|
2.4
|
32.8
|
1.0
|
N10
|
A:YK1301
|
2.9
|
31.9
|
1.0
|
C11
|
A:YK1301
|
3.0
|
33.9
|
1.0
|
O
|
A:HOH549
|
3.2
|
41.1
|
1.0
|
O
|
A:HOH449
|
3.2
|
44.6
|
1.0
|
CB
|
A:ASP155
|
3.4
|
39.6
|
1.0
|
O8
|
A:YK1301
|
3.4
|
30.2
|
1.0
|
C13
|
A:YK1301
|
3.5
|
32.7
|
1.0
|
N
|
A:ASP155
|
3.5
|
32.8
|
1.0
|
CA
|
A:ASP155
|
3.8
|
37.6
|
1.0
|
CB
|
A:ALA154
|
4.0
|
31.8
|
1.0
|
CG
|
A:ASP155
|
4.1
|
44.8
|
1.0
|
C4
|
A:YK1301
|
4.1
|
28.3
|
1.0
|
OD2
|
A:ASP155
|
4.2
|
59.7
|
1.0
|
C16
|
A:YK1301
|
4.3
|
32.2
|
1.0
|
C
|
A:ALA154
|
4.4
|
32.3
|
1.0
|
C7
|
A:YK1301
|
4.5
|
30.1
|
1.0
|
C14
|
A:YK1301
|
4.7
|
33.8
|
1.0
|
C5
|
A:YK1301
|
4.7
|
27.6
|
1.0
|
CA
|
A:ALA154
|
4.8
|
30.4
|
1.0
|
O
|
A:HOH484
|
4.9
|
44.6
|
1.0
|
OD1
|
A:ASP155
|
4.9
|
47.2
|
1.0
|
CD1
|
A:LEU144
|
4.9
|
31.5
|
1.0
|
|
Fluorine binding site 3 out
of 8 in 7m0m
Go back to
Fluorine Binding Sites List in 7m0m
Fluorine binding site 3 out
of 8 in the HPK1 in Complex with Compound 1
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of HPK1 in Complex with Compound 1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F301
b:41.2
occ:1.00
|
F20
|
A:YK1301
|
0.0
|
41.2
|
1.0
|
C18
|
A:YK1301
|
1.4
|
36.8
|
1.0
|
F21
|
A:YK1301
|
2.2
|
34.5
|
1.0
|
F19
|
A:YK1301
|
2.3
|
37.7
|
1.0
|
C12
|
A:YK1301
|
2.4
|
32.8
|
1.0
|
C13
|
A:YK1301
|
2.8
|
32.7
|
1.0
|
OD1
|
A:ASN142
|
3.2
|
36.0
|
1.0
|
CB
|
A:ASP155
|
3.3
|
39.6
|
1.0
|
OD2
|
A:ASP155
|
3.5
|
59.7
|
1.0
|
C11
|
A:YK1301
|
3.7
|
33.9
|
1.0
|
CG
|
A:ASP155
|
3.9
|
44.8
|
1.0
|
O
|
A:ALA141
|
3.9
|
28.8
|
1.0
|
C14
|
A:YK1301
|
4.1
|
33.8
|
1.0
|
O
|
A:HOH434
|
4.2
|
35.0
|
1.0
|
O
|
A:HOH572
|
4.2
|
45.2
|
1.0
|
N10
|
A:YK1301
|
4.3
|
31.9
|
1.0
|
CA
|
A:GLY26
|
4.3
|
43.5
|
1.0
|
CG
|
A:ASN142
|
4.4
|
32.4
|
1.0
|
CA
|
A:ASP155
|
4.4
|
37.6
|
1.0
|
N
|
A:ASP155
|
4.5
|
32.8
|
1.0
|
O
|
A:HOH549
|
4.5
|
41.1
|
1.0
|
CA
|
A:ASN142
|
4.6
|
27.6
|
1.0
|
C
|
A:ALA141
|
4.8
|
29.9
|
1.0
|
CB
|
A:ALA154
|
4.8
|
31.8
|
1.0
|
C16
|
A:YK1301
|
4.8
|
32.2
|
1.0
|
C
|
A:ALA154
|
4.9
|
32.3
|
1.0
|
CB
|
A:ASN142
|
5.0
|
30.3
|
1.0
|
|
Fluorine binding site 4 out
of 8 in 7m0m
Go back to
Fluorine Binding Sites List in 7m0m
Fluorine binding site 4 out
of 8 in the HPK1 in Complex with Compound 1
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of HPK1 in Complex with Compound 1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F301
b:34.5
occ:1.00
|
F21
|
A:YK1301
|
0.0
|
34.5
|
1.0
|
C18
|
A:YK1301
|
1.4
|
36.8
|
1.0
|
F20
|
A:YK1301
|
2.2
|
41.2
|
1.0
|
F19
|
A:YK1301
|
2.2
|
37.7
|
1.0
|
C12
|
A:YK1301
|
2.3
|
32.8
|
1.0
|
C11
|
A:YK1301
|
2.9
|
33.9
|
1.0
|
N10
|
A:YK1301
|
2.9
|
31.9
|
1.0
|
CD2
|
A:LEU144
|
3.4
|
33.2
|
1.0
|
C13
|
A:YK1301
|
3.4
|
32.7
|
1.0
|
CD1
|
A:LEU144
|
3.4
|
31.5
|
1.0
|
CB
|
A:ALA154
|
3.5
|
31.8
|
1.0
|
C4
|
A:YK1301
|
3.6
|
28.3
|
1.0
|
CG
|
A:LEU144
|
3.7
|
31.1
|
1.0
|
N3
|
A:YK1301
|
4.1
|
24.2
|
1.0
|
O8
|
A:YK1301
|
4.1
|
30.2
|
1.0
|
C16
|
A:YK1301
|
4.2
|
32.2
|
1.0
|
O
|
A:ALA141
|
4.2
|
28.8
|
1.0
|
C5
|
A:YK1301
|
4.4
|
27.6
|
1.0
|
N
|
A:ASP155
|
4.5
|
32.8
|
1.0
|
C14
|
A:YK1301
|
4.6
|
33.8
|
1.0
|
CB
|
A:ASP155
|
4.6
|
39.6
|
1.0
|
O
|
A:HOH449
|
4.6
|
44.6
|
1.0
|
O
|
A:HOH434
|
4.6
|
35.0
|
1.0
|
C7
|
A:YK1301
|
4.7
|
30.1
|
1.0
|
CA
|
A:ALA154
|
4.8
|
30.4
|
1.0
|
C
|
A:ALA154
|
4.8
|
32.3
|
1.0
|
OD1
|
A:ASN142
|
4.8
|
36.0
|
1.0
|
C15
|
A:YK1301
|
4.9
|
35.6
|
1.0
|
CA
|
A:ASN142
|
4.9
|
27.6
|
1.0
|
|
Fluorine binding site 5 out
of 8 in 7m0m
Go back to
Fluorine Binding Sites List in 7m0m
Fluorine binding site 5 out
of 8 in the HPK1 in Complex with Compound 1
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of HPK1 in Complex with Compound 1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F301
b:31.7
occ:1.00
|
F17
|
B:YK1301
|
0.0
|
31.7
|
1.0
|
C16
|
B:YK1301
|
1.3
|
32.9
|
1.0
|
C15
|
B:YK1301
|
2.3
|
35.3
|
1.0
|
C11
|
B:YK1301
|
2.4
|
31.2
|
1.0
|
N10
|
B:YK1301
|
2.8
|
31.5
|
1.0
|
N3
|
B:YK1301
|
2.8
|
22.4
|
1.0
|
C4
|
B:YK1301
|
3.0
|
26.3
|
1.0
|
CB
|
B:VAL31
|
3.1
|
31.5
|
1.0
|
CG1
|
B:VAL31
|
3.1
|
32.7
|
1.0
|
CB
|
B:LEU23
|
3.3
|
38.4
|
1.0
|
CD1
|
B:LEU23
|
3.4
|
34.5
|
1.0
|
C14
|
B:YK1301
|
3.6
|
35.9
|
1.0
|
CG2
|
B:VAL31
|
3.6
|
32.4
|
1.0
|
C12
|
B:YK1301
|
3.6
|
34.5
|
1.0
|
C24
|
B:YK1301
|
3.7
|
35.0
|
1.0
|
C2
|
B:YK1301
|
3.8
|
25.9
|
1.0
|
CG
|
B:LEU23
|
4.0
|
39.2
|
1.0
|
C13
|
B:YK1301
|
4.1
|
33.3
|
1.0
|
C23
|
B:YK1301
|
4.2
|
33.7
|
1.0
|
C5
|
B:YK1301
|
4.2
|
26.9
|
1.0
|
N22
|
B:YK1301
|
4.3
|
29.8
|
1.0
|
CA
|
B:VAL31
|
4.4
|
33.5
|
1.0
|
C25
|
B:YK1301
|
4.4
|
36.6
|
1.0
|
CA
|
B:LEU23
|
4.6
|
40.1
|
1.0
|
C
|
B:LEU23
|
4.6
|
39.8
|
1.0
|
O
|
B:VAL31
|
4.6
|
33.6
|
1.0
|
C
|
B:VAL31
|
4.6
|
33.0
|
1.0
|
C34
|
B:YK1301
|
4.7
|
34.1
|
1.0
|
N1
|
B:YK1301
|
4.7
|
26.2
|
1.0
|
O
|
B:GLY24
|
4.8
|
47.9
|
1.0
|
O
|
B:LEU23
|
4.8
|
45.8
|
1.0
|
C6
|
B:YK1301
|
4.9
|
22.6
|
1.0
|
C18
|
B:YK1301
|
4.9
|
30.7
|
1.0
|
N
|
B:GLY24
|
4.9
|
42.0
|
1.0
|
|
Fluorine binding site 6 out
of 8 in 7m0m
Go back to
Fluorine Binding Sites List in 7m0m
Fluorine binding site 6 out
of 8 in the HPK1 in Complex with Compound 1
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of HPK1 in Complex with Compound 1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F301
b:36.4
occ:1.00
|
F19
|
B:YK1301
|
0.0
|
36.4
|
1.0
|
C18
|
B:YK1301
|
1.4
|
30.7
|
1.0
|
F21
|
B:YK1301
|
2.2
|
35.2
|
1.0
|
F20
|
B:YK1301
|
2.3
|
36.5
|
1.0
|
C12
|
B:YK1301
|
2.4
|
34.5
|
1.0
|
N10
|
B:YK1301
|
2.9
|
31.5
|
1.0
|
C11
|
B:YK1301
|
3.0
|
31.2
|
1.0
|
O
|
B:HOH456
|
3.2
|
36.1
|
1.0
|
O8
|
B:YK1301
|
3.3
|
29.4
|
1.0
|
O
|
B:HOH447
|
3.5
|
46.5
|
1.0
|
C13
|
B:YK1301
|
3.5
|
33.3
|
1.0
|
CB
|
B:ASP155
|
3.5
|
33.4
|
1.0
|
N
|
B:ASP155
|
3.8
|
28.9
|
1.0
|
CA
|
B:ASP155
|
3.9
|
34.0
|
1.0
|
CB
|
B:ALA154
|
4.0
|
33.8
|
1.0
|
C4
|
B:YK1301
|
4.0
|
26.3
|
1.0
|
CG
|
B:ASP155
|
4.1
|
36.7
|
1.0
|
OD2
|
B:ASP155
|
4.2
|
37.4
|
1.0
|
C16
|
B:YK1301
|
4.3
|
32.9
|
1.0
|
C7
|
B:YK1301
|
4.3
|
26.5
|
1.0
|
C
|
B:ALA154
|
4.5
|
31.6
|
1.0
|
C5
|
B:YK1301
|
4.6
|
26.9
|
1.0
|
O
|
B:HOH462
|
4.6
|
52.7
|
1.0
|
C14
|
B:YK1301
|
4.7
|
35.9
|
1.0
|
CA
|
B:ALA154
|
4.9
|
33.0
|
1.0
|
CA
|
B:GLY26
|
4.9
|
43.5
|
1.0
|
N3
|
B:YK1301
|
5.0
|
22.4
|
1.0
|
OD1
|
B:ASP155
|
5.0
|
37.7
|
1.0
|
|
Fluorine binding site 7 out
of 8 in 7m0m
Go back to
Fluorine Binding Sites List in 7m0m
Fluorine binding site 7 out
of 8 in the HPK1 in Complex with Compound 1
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 7 of HPK1 in Complex with Compound 1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F301
b:36.5
occ:1.00
|
F20
|
B:YK1301
|
0.0
|
36.5
|
1.0
|
C18
|
B:YK1301
|
1.4
|
30.7
|
1.0
|
F21
|
B:YK1301
|
2.3
|
35.2
|
1.0
|
F19
|
B:YK1301
|
2.3
|
36.4
|
1.0
|
C12
|
B:YK1301
|
2.4
|
34.5
|
1.0
|
C13
|
B:YK1301
|
2.8
|
33.3
|
1.0
|
O
|
B:HOH407
|
3.1
|
41.0
|
1.0
|
OD1
|
B:ASN142
|
3.2
|
35.0
|
1.0
|
CB
|
B:ASP155
|
3.4
|
33.4
|
1.0
|
OD2
|
B:ASP155
|
3.4
|
37.4
|
1.0
|
C11
|
B:YK1301
|
3.7
|
31.2
|
1.0
|
CG
|
B:ASP155
|
3.8
|
36.7
|
1.0
|
O
|
B:HOH544
|
3.9
|
40.6
|
1.0
|
CA
|
B:GLY26
|
4.1
|
43.5
|
1.0
|
O
|
B:ALA141
|
4.1
|
32.8
|
1.0
|
C14
|
B:YK1301
|
4.1
|
35.9
|
1.0
|
O
|
B:HOH414
|
4.3
|
36.3
|
1.0
|
N10
|
B:YK1301
|
4.3
|
31.5
|
1.0
|
CG
|
B:ASN142
|
4.4
|
33.6
|
1.0
|
CA
|
B:ASP155
|
4.5
|
34.0
|
1.0
|
O
|
B:HOH456
|
4.6
|
36.1
|
1.0
|
N
|
B:ASP155
|
4.6
|
28.9
|
1.0
|
N
|
B:GLY26
|
4.8
|
45.9
|
1.0
|
CA
|
B:ASN142
|
4.8
|
31.4
|
1.0
|
C16
|
B:YK1301
|
4.8
|
32.9
|
1.0
|
CB
|
B:ALA154
|
4.9
|
33.8
|
1.0
|
OD1
|
B:ASP155
|
5.0
|
37.7
|
1.0
|
C
|
B:ALA141
|
5.0
|
34.1
|
1.0
|
C
|
B:ALA154
|
5.0
|
31.6
|
1.0
|
|
Fluorine binding site 8 out
of 8 in 7m0m
Go back to
Fluorine Binding Sites List in 7m0m
Fluorine binding site 8 out
of 8 in the HPK1 in Complex with Compound 1
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 8 of HPK1 in Complex with Compound 1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F301
b:35.2
occ:1.00
|
F21
|
B:YK1301
|
0.0
|
35.2
|
1.0
|
C18
|
B:YK1301
|
1.4
|
30.7
|
1.0
|
F19
|
B:YK1301
|
2.2
|
36.4
|
1.0
|
F20
|
B:YK1301
|
2.3
|
36.5
|
1.0
|
C12
|
B:YK1301
|
2.3
|
34.5
|
1.0
|
C11
|
B:YK1301
|
2.9
|
31.2
|
1.0
|
N10
|
B:YK1301
|
3.0
|
31.5
|
1.0
|
C13
|
B:YK1301
|
3.4
|
33.3
|
1.0
|
CD2
|
B:LEU144
|
3.5
|
34.0
|
1.0
|
CD1
|
B:LEU144
|
3.5
|
33.1
|
1.0
|
CB
|
B:ALA154
|
3.5
|
33.8
|
1.0
|
C4
|
B:YK1301
|
3.6
|
26.3
|
1.0
|
CG
|
B:LEU144
|
3.8
|
31.3
|
1.0
|
O8
|
B:YK1301
|
4.1
|
29.4
|
1.0
|
N3
|
B:YK1301
|
4.1
|
22.4
|
1.0
|
O
|
B:ALA141
|
4.2
|
32.8
|
1.0
|
C16
|
B:YK1301
|
4.3
|
32.9
|
1.0
|
C5
|
B:YK1301
|
4.4
|
26.9
|
1.0
|
O
|
B:HOH414
|
4.6
|
36.3
|
1.0
|
C14
|
B:YK1301
|
4.6
|
35.9
|
1.0
|
CB
|
B:ASP155
|
4.6
|
33.4
|
1.0
|
OD1
|
B:ASN142
|
4.6
|
35.0
|
1.0
|
N
|
B:ASP155
|
4.6
|
28.9
|
1.0
|
C7
|
B:YK1301
|
4.6
|
26.5
|
1.0
|
CA
|
B:ALA154
|
4.7
|
33.0
|
1.0
|
C
|
B:ALA154
|
4.8
|
31.6
|
1.0
|
CA
|
B:ASN142
|
4.9
|
31.4
|
1.0
|
C15
|
B:YK1301
|
4.9
|
35.3
|
1.0
|
|
Reference:
B.A.Vara,
S.M.Levi,
A.Achab,
D.A.Candito,
X.Fradera,
C.Lesburg,
S.Kawamura,
B.M.Lacey,
J.Lim,
J.L.Methot,
Z.Xu,
H.Xu,
D.M.Smith,
J.Piesvaux,
J.R.Miller,
M.Bittinger,
J.Bennett,
E.F.Dimauro,
A.Pasternak.
Discovery of Diaminopyrimidine Carboxamide HPK1 Inhibitors As Preclinical Immunotherapy Tool Compounds Acs Med.Chem.Lett. 2021.
ISSN: ISSN 1948-5875
DOI: 10.1021/ACSMEDCHEMLETT.1C00096
Page generated: Fri Aug 2 09:12:22 2024
|