Magnesium in PDB 8p5h: Kinase Domain of Mutant Human ULK1 in Complex with Compound CCT241533
Enzymatic activity of Kinase Domain of Mutant Human ULK1 in Complex with Compound CCT241533
All present enzymatic activity of Kinase Domain of Mutant Human ULK1 in Complex with Compound CCT241533:
2.7.11.1;
Protein crystallography data
The structure of Kinase Domain of Mutant Human ULK1 in Complex with Compound CCT241533, PDB code: 8p5h
was solved by
T.Battista,
M.S.Semrau,
A.Heroux,
G.Lolli,
P.Storici,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
66.90 /
1.94
|
|
Space group
|
P 2 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
84.65,
96.31,
109.19,
90,
90,
90
|
|
R / Rfree (%)
|
17 /
19.3
|
Other elements in 8p5h:
The structure of Kinase Domain of Mutant Human ULK1 in Complex with Compound CCT241533 also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Kinase Domain of Mutant Human ULK1 in Complex with Compound CCT241533
(pdb code 8p5h). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Kinase Domain of Mutant Human ULK1 in Complex with Compound CCT241533, PDB code: 8p5h:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 8p5h
Go back to
Magnesium Binding Sites List in 8p5h
Magnesium binding site 1 out
of 4 in the Kinase Domain of Mutant Human ULK1 in Complex with Compound CCT241533
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Kinase Domain of Mutant Human ULK1 in Complex with Compound CCT241533 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg302
b:40.5
occ:1.00
|
H
|
A:ASP199
|
2.0
|
26.9
|
1.0
|
|
OE2
|
A:GLU191
|
2.8
|
30.0
|
1.0
|
|
HB2
|
A:TYR198
|
2.8
|
25.1
|
1.0
|
|
OD1
|
A:ASP199
|
2.8
|
31.5
|
1.0
|
|
N
|
A:ASP199
|
2.9
|
25.6
|
1.0
|
|
HA
|
A:TYR198
|
3.0
|
26.7
|
1.0
|
|
HG3
|
A:GLU191
|
3.1
|
30.9
|
1.0
|
|
HB2
|
A:HIS263
|
3.1
|
36.9
|
1.0
|
|
HB2
|
A:LYS201
|
3.3
|
32.6
|
1.0
|
|
H
|
A:ALA202
|
3.3
|
27.6
|
1.0
|
|
HB3
|
A:HIS263
|
3.4
|
36.9
|
1.0
|
|
HB2
|
A:ALA202
|
3.4
|
26.5
|
1.0
|
|
CB
|
A:TYR198
|
3.5
|
25.5
|
1.0
|
|
CA
|
A:TYR198
|
3.5
|
26.1
|
1.0
|
|
CB
|
A:HIS263
|
3.6
|
37.0
|
1.0
|
|
CG
|
A:ASP199
|
3.6
|
32.7
|
1.0
|
|
CG
|
A:HIS263
|
3.6
|
38.2
|
1.0
|
|
CD
|
A:GLU191
|
3.6
|
31.9
|
1.0
|
|
HH12
|
A:ARG266
|
3.7
|
29.6
|
1.0
|
|
O
|
A:ASP199
|
3.7
|
24.6
|
1.0
|
|
N
|
A:ALA202
|
3.7
|
28.0
|
1.0
|
|
C
|
A:TYR198
|
3.7
|
29.2
|
1.0
|
|
CG
|
A:GLU191
|
3.8
|
31.1
|
1.0
|
|
HB3
|
A:TYR198
|
3.8
|
25.1
|
1.0
|
|
CA
|
A:ASP199
|
3.9
|
27.3
|
1.0
|
|
H
|
A:LYS201
|
3.9
|
28.2
|
1.0
|
|
ND1
|
A:HIS263
|
4.0
|
41.0
|
1.0
|
|
C
|
A:ASP199
|
4.0
|
27.0
|
1.0
|
|
CD2
|
A:HIS263
|
4.0
|
45.7
|
1.0
|
|
HG2
|
A:GLU191
|
4.1
|
31.0
|
1.0
|
|
HE3
|
A:MET177
|
4.1
|
31.0
|
0.5
|
|
HD1
|
A:HIS263
|
4.1
|
40.7
|
0.0
|
|
CB
|
A:LYS201
|
4.2
|
31.6
|
1.0
|
|
C
|
A:LYS201
|
4.2
|
27.4
|
1.0
|
|
CB
|
A:ASP199
|
4.2
|
27.3
|
1.0
|
|
HA
|
A:ALA202
|
4.2
|
27.2
|
1.0
|
|
CB
|
A:ALA202
|
4.3
|
26.3
|
1.0
|
|
HD2
|
A:HIS263
|
4.3
|
43.1
|
1.0
|
|
OD2
|
A:ASP199
|
4.3
|
34.1
|
1.0
|
|
CA
|
A:ALA202
|
4.3
|
26.8
|
1.0
|
|
N
|
A:LYS201
|
4.3
|
26.7
|
1.0
|
|
CA
|
A:LYS201
|
4.5
|
30.9
|
1.0
|
|
HD1
|
A:TYR198
|
4.5
|
21.6
|
1.0
|
|
NH1
|
A:ARG266
|
4.5
|
29.7
|
1.0
|
|
CE1
|
A:HIS263
|
4.5
|
45.9
|
1.0
|
|
HB3
|
A:ASP199
|
4.6
|
28.5
|
1.0
|
|
HB3
|
A:LYS201
|
4.6
|
32.6
|
1.0
|
|
NE2
|
A:HIS263
|
4.6
|
42.5
|
1.0
|
|
HB3
|
A:ALA202
|
4.7
|
26.6
|
1.0
|
|
HA
|
A:ASP199
|
4.7
|
26.9
|
1.0
|
|
HH11
|
A:ARG266
|
4.8
|
29.6
|
1.0
|
|
CG
|
A:TYR198
|
4.8
|
22.9
|
1.0
|
|
OE1
|
A:GLU191
|
4.8
|
30.4
|
1.0
|
|
HE2
|
A:MET177
|
4.8
|
30.7
|
0.5
|
|
N
|
A:TYR198
|
4.9
|
26.9
|
1.0
|
|
HE1
|
A:MET177
|
4.9
|
30.7
|
0.5
|
|
N
|
A:GLY200
|
4.9
|
25.0
|
1.0
|
|
O
|
A:TYR198
|
4.9
|
24.7
|
1.0
|
|
O
|
A:HIS197
|
4.9
|
26.3
|
1.0
|
|
HB1
|
A:ALA202
|
5.0
|
26.5
|
1.0
|
|
CE
|
A:MET177
|
5.0
|
29.6
|
0.5
|
|
HE2
|
A:MET177
|
5.0
|
31.0
|
0.5
|
|
Magnesium binding site 2 out
of 4 in 8p5h
Go back to
Magnesium Binding Sites List in 8p5h
Magnesium binding site 2 out
of 4 in the Kinase Domain of Mutant Human ULK1 in Complex with Compound CCT241533
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Kinase Domain of Mutant Human ULK1 in Complex with Compound CCT241533 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg303
b:34.3
occ:1.00
|
H
|
A:PHE168
|
2.2
|
25.0
|
1.0
|
|
HA
|
A:PHE166
|
2.6
|
26.2
|
1.0
|
|
HB2
|
A:PHE168
|
2.7
|
25.9
|
1.0
|
|
O
|
A:ASP165
|
2.8
|
25.1
|
1.0
|
|
O
|
A:HIS136
|
2.9
|
20.5
|
1.0
|
|
N
|
A:PHE168
|
2.9
|
24.6
|
1.0
|
|
H
|
A:ALA169
|
3.0
|
19.9
|
1.0
|
|
C
|
A:PHE166
|
3.3
|
27.2
|
1.0
|
|
CA
|
A:PHE166
|
3.3
|
26.1
|
1.0
|
|
N
|
A:ALA169
|
3.3
|
19.7
|
1.0
|
|
HB3
|
A:ASP138
|
3.4
|
27.1
|
1.0
|
|
CE1
|
A:HIS136
|
3.4
|
20.9
|
1.0
|
|
H
|
A:GLY167
|
3.4
|
26.4
|
1.0
|
|
N
|
A:GLY167
|
3.4
|
25.9
|
1.0
|
|
HD2
|
A:PHE168
|
3.4
|
36.7
|
1.0
|
|
CB
|
A:PHE168
|
3.5
|
25.7
|
1.0
|
|
HE1
|
A:HIS136
|
3.5
|
21.0
|
1.0
|
|
CA
|
A:PHE168
|
3.5
|
22.9
|
1.0
|
|
HB2
|
A:ALA169
|
3.6
|
20.6
|
1.0
|
|
ND1
|
A:HIS136
|
3.6
|
21.1
|
1.0
|
|
HB2
|
A:ASP138
|
3.6
|
27.1
|
1.0
|
|
C
|
A:PHE168
|
3.7
|
21.1
|
1.0
|
|
HD1
|
A:HIS136
|
3.7
|
21.0
|
0.0
|
|
C
|
A:ASP165
|
3.8
|
26.7
|
1.0
|
|
O
|
A:PHE166
|
3.8
|
26.5
|
1.0
|
|
NE2
|
A:HIS136
|
3.9
|
20.9
|
1.0
|
|
O
|
A:HOH468
|
3.9
|
44.4
|
1.0
|
|
C
|
A:HIS136
|
3.9
|
20.7
|
1.0
|
|
N
|
A:PHE166
|
3.9
|
26.6
|
1.0
|
|
H
|
A:ASP138
|
4.0
|
24.2
|
1.0
|
|
CB
|
A:ASP138
|
4.0
|
26.0
|
1.0
|
|
C
|
A:GLY167
|
4.0
|
27.5
|
1.0
|
|
HB3
|
A:PHE168
|
4.1
|
25.8
|
1.0
|
|
CD2
|
A:PHE168
|
4.2
|
39.4
|
1.0
|
|
CG
|
A:HIS136
|
4.2
|
19.8
|
1.0
|
|
HE2
|
A:HIS136
|
4.2
|
20.9
|
0.0
|
|
CA
|
A:ALA169
|
4.2
|
18.4
|
1.0
|
|
CA
|
A:GLY167
|
4.2
|
26.7
|
1.0
|
|
HA
|
A:ALA169
|
4.2
|
19.7
|
1.0
|
|
CB
|
A:ALA169
|
4.3
|
21.6
|
1.0
|
|
CD2
|
A:HIS136
|
4.3
|
19.3
|
1.0
|
|
N
|
A:ASP138
|
4.3
|
23.7
|
1.0
|
|
CG
|
A:PHE168
|
4.3
|
29.2
|
1.0
|
|
HA
|
A:HIS136
|
4.3
|
21.4
|
1.0
|
|
HA
|
A:PHE168
|
4.4
|
23.5
|
1.0
|
|
HB2
|
A:ARG137
|
4.5
|
23.5
|
1.0
|
|
HB3
|
A:ALA169
|
4.5
|
20.7
|
1.0
|
|
CB
|
A:PHE166
|
4.6
|
24.8
|
1.0
|
|
O
|
A:PHE168
|
4.6
|
22.2
|
1.0
|
|
CA
|
A:HIS136
|
4.6
|
21.4
|
1.0
|
|
HB3
|
A:PHE166
|
4.7
|
25.0
|
1.0
|
|
HA3
|
A:GLY167
|
4.7
|
26.7
|
1.0
|
|
CA
|
A:ASP138
|
4.7
|
24.9
|
1.0
|
|
O
|
A:HOH510
|
4.8
|
39.9
|
1.0
|
|
H
|
A:PHE166
|
4.8
|
26.5
|
1.0
|
|
N
|
A:ARG137
|
4.8
|
20.6
|
1.0
|
|
C
|
A:ARG137
|
4.9
|
25.1
|
1.0
|
|
HD2
|
A:HIS136
|
4.9
|
19.8
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 8p5h
Go back to
Magnesium Binding Sites List in 8p5h
Magnesium binding site 3 out
of 4 in the Kinase Domain of Mutant Human ULK1 in Complex with Compound CCT241533
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Kinase Domain of Mutant Human ULK1 in Complex with Compound CCT241533 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg302
b:37.0
occ:1.00
|
H
|
B:ASP199
|
2.0
|
24.5
|
1.0
|
|
HB2
|
B:TYR198
|
2.7
|
23.0
|
1.0
|
|
OE2
|
B:GLU191
|
2.7
|
25.0
|
1.0
|
|
OD1
|
B:ASP199
|
2.9
|
26.7
|
1.0
|
|
N
|
B:ASP199
|
2.9
|
23.5
|
1.0
|
|
HB2
|
B:HIS263
|
3.0
|
29.3
|
1.0
|
|
HA
|
B:TYR198
|
3.0
|
24.4
|
1.0
|
|
HG3
|
B:GLU191
|
3.0
|
26.5
|
1.0
|
|
HB3
|
B:HIS263
|
3.3
|
29.2
|
1.0
|
|
HB2
|
B:LYS201
|
3.3
|
28.9
|
1.0
|
|
H
|
B:ALA202
|
3.3
|
23.0
|
1.0
|
|
HB2
|
B:ALA202
|
3.3
|
24.8
|
1.0
|
|
CB
|
B:HIS263
|
3.5
|
28.2
|
1.0
|
|
CB
|
B:TYR198
|
3.5
|
23.4
|
1.0
|
|
CA
|
B:TYR198
|
3.5
|
24.0
|
1.0
|
|
CG
|
B:HIS263
|
3.6
|
31.5
|
1.0
|
|
CD
|
B:GLU191
|
3.6
|
30.1
|
1.0
|
|
HH12
|
B:ARG266
|
3.6
|
24.4
|
1.0
|
|
N
|
B:ALA202
|
3.6
|
22.0
|
1.0
|
|
O
|
B:ASP199
|
3.6
|
23.6
|
1.0
|
|
CG
|
B:ASP199
|
3.7
|
30.7
|
1.0
|
|
CG
|
B:GLU191
|
3.7
|
25.5
|
1.0
|
|
HB3
|
B:TYR198
|
3.7
|
23.0
|
1.0
|
|
C
|
B:TYR198
|
3.7
|
25.0
|
1.0
|
|
CA
|
B:ASP199
|
3.9
|
26.1
|
1.0
|
|
ND1
|
B:HIS263
|
3.9
|
36.3
|
1.0
|
|
C
|
B:ASP199
|
4.0
|
25.3
|
1.0
|
|
HG2
|
B:GLU191
|
4.0
|
26.5
|
1.0
|
|
H
|
B:LYS201
|
4.0
|
24.3
|
1.0
|
|
CD2
|
B:HIS263
|
4.1
|
34.8
|
1.0
|
|
HD1
|
B:HIS263
|
4.1
|
36.4
|
0.0
|
|
HA
|
B:ALA202
|
4.1
|
24.3
|
1.0
|
|
CB
|
B:ALA202
|
4.1
|
25.1
|
1.0
|
|
CB
|
B:LYS201
|
4.2
|
28.5
|
1.0
|
|
C
|
B:LYS201
|
4.2
|
24.5
|
1.0
|
|
CA
|
B:ALA202
|
4.2
|
23.7
|
1.0
|
|
HE3
|
B:MET177
|
4.3
|
31.2
|
0.5
|
|
CB
|
B:ASP199
|
4.3
|
28.8
|
1.0
|
|
HD2
|
B:HIS263
|
4.3
|
34.5
|
1.0
|
|
N
|
B:LYS201
|
4.3
|
23.3
|
1.0
|
|
NH1
|
B:ARG266
|
4.4
|
23.8
|
1.0
|
|
OD2
|
B:ASP199
|
4.4
|
33.5
|
1.0
|
|
CA
|
B:LYS201
|
4.4
|
26.0
|
1.0
|
|
HD2
|
B:TYR198
|
4.4
|
21.9
|
1.0
|
|
HB3
|
B:LYS201
|
4.5
|
28.9
|
1.0
|
|
HB3
|
B:ALA202
|
4.6
|
24.9
|
1.0
|
|
CE1
|
B:HIS263
|
4.6
|
35.9
|
1.0
|
|
HB3
|
B:ASP199
|
4.6
|
28.6
|
1.0
|
|
NE2
|
B:HIS263
|
4.6
|
37.3
|
1.0
|
|
HH11
|
B:ARG266
|
4.7
|
24.4
|
1.0
|
|
CG
|
B:TYR198
|
4.7
|
21.0
|
1.0
|
|
OE1
|
B:GLU191
|
4.7
|
26.2
|
1.0
|
|
HA
|
B:ASP199
|
4.7
|
25.8
|
1.0
|
|
O
|
B:HOH416
|
4.8
|
38.8
|
1.0
|
|
HB1
|
B:ALA202
|
4.9
|
24.8
|
1.0
|
|
N
|
B:TYR198
|
4.9
|
25.9
|
1.0
|
|
N
|
B:GLY200
|
4.9
|
26.3
|
1.0
|
|
CA
|
B:HIS263
|
4.9
|
29.7
|
1.0
|
|
O
|
B:TYR198
|
5.0
|
22.6
|
1.0
|
|
HE2
|
B:MET177
|
5.0
|
25.5
|
0.5
|
|
CD2
|
B:TYR198
|
5.0
|
22.4
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 8p5h
Go back to
Magnesium Binding Sites List in 8p5h
Magnesium binding site 4 out
of 4 in the Kinase Domain of Mutant Human ULK1 in Complex with Compound CCT241533
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Kinase Domain of Mutant Human ULK1 in Complex with Compound CCT241533 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg303
b:35.1
occ:1.00
|
H
|
B:PHE168
|
2.2
|
25.0
|
1.0
|
|
HA
|
B:PHE166
|
2.6
|
25.5
|
1.0
|
|
HB2
|
B:PHE168
|
2.8
|
26.2
|
1.0
|
|
O
|
B:ASP165
|
2.8
|
26.5
|
1.0
|
|
O
|
B:HIS136
|
2.9
|
22.3
|
1.0
|
|
H
|
B:ALA169
|
3.0
|
22.7
|
1.0
|
|
N
|
B:PHE168
|
3.0
|
24.8
|
1.0
|
|
HB3
|
B:ASP138
|
3.3
|
29.6
|
1.0
|
|
CA
|
B:PHE166
|
3.3
|
25.4
|
1.0
|
|
C
|
B:PHE166
|
3.3
|
25.3
|
1.0
|
|
N
|
B:ALA169
|
3.4
|
22.7
|
1.0
|
|
CE1
|
B:HIS136
|
3.4
|
25.5
|
1.0
|
|
HD2
|
B:PHE168
|
3.4
|
38.5
|
1.0
|
|
H
|
B:GLY167
|
3.4
|
26.4
|
1.0
|
|
N
|
B:GLY167
|
3.4
|
26.1
|
1.0
|
|
HE1
|
B:HIS136
|
3.5
|
24.9
|
1.0
|
|
HB2
|
B:ALA169
|
3.5
|
22.6
|
1.0
|
|
CA
|
B:PHE168
|
3.5
|
22.4
|
1.0
|
|
CB
|
B:PHE168
|
3.6
|
26.1
|
1.0
|
|
ND1
|
B:HIS136
|
3.6
|
24.5
|
1.0
|
|
HB2
|
B:ASP138
|
3.7
|
29.7
|
1.0
|
|
C
|
B:PHE168
|
3.7
|
22.3
|
1.0
|
|
C
|
B:ASP165
|
3.8
|
31.2
|
1.0
|
|
HD1
|
B:HIS136
|
3.8
|
24.5
|
0.0
|
|
O
|
B:HOH503
|
3.8
|
46.6
|
1.0
|
|
O
|
B:PHE166
|
3.8
|
25.9
|
1.0
|
|
NE2
|
B:HIS136
|
3.9
|
24.2
|
1.0
|
|
H
|
B:ASP138
|
3.9
|
25.6
|
1.0
|
|
C
|
B:HIS136
|
3.9
|
23.6
|
1.0
|
|
CB
|
B:ASP138
|
4.0
|
27.6
|
1.0
|
|
N
|
B:PHE166
|
4.0
|
27.9
|
1.0
|
|
C
|
B:GLY167
|
4.0
|
27.7
|
1.0
|
|
CG
|
B:HIS136
|
4.1
|
21.3
|
1.0
|
|
CD2
|
B:PHE168
|
4.2
|
40.8
|
1.0
|
|
HE2
|
B:HIS136
|
4.2
|
24.1
|
0.0
|
|
CD2
|
B:HIS136
|
4.2
|
22.6
|
1.0
|
|
CA
|
B:ALA169
|
4.2
|
22.8
|
1.0
|
|
N
|
B:ASP138
|
4.2
|
24.6
|
1.0
|
|
HA
|
B:ALA169
|
4.3
|
23.0
|
1.0
|
|
CB
|
B:ALA169
|
4.3
|
22.5
|
1.0
|
|
CA
|
B:GLY167
|
4.3
|
28.4
|
1.0
|
|
HB3
|
B:PHE168
|
4.3
|
26.1
|
1.0
|
|
HA
|
B:HIS136
|
4.3
|
22.5
|
1.0
|
|
CG
|
B:PHE168
|
4.4
|
30.4
|
1.0
|
|
HA
|
B:PHE168
|
4.5
|
23.6
|
1.0
|
|
HB2
|
B:ARG137
|
4.5
|
23.5
|
1.0
|
|
CB
|
B:PHE166
|
4.6
|
23.4
|
1.0
|
|
HB3
|
B:ALA169
|
4.6
|
22.7
|
1.0
|
|
CA
|
B:HIS136
|
4.6
|
21.2
|
1.0
|
|
O
|
B:PHE168
|
4.6
|
22.2
|
1.0
|
|
CA
|
B:ASP138
|
4.7
|
29.1
|
1.0
|
|
HB3
|
B:PHE166
|
4.7
|
23.6
|
1.0
|
|
HA3
|
B:GLY167
|
4.7
|
27.7
|
1.0
|
|
O
|
B:HOH512
|
4.8
|
41.2
|
1.0
|
|
HB3
|
B:ASP165
|
4.8
|
36.1
|
0.5
|
|
N
|
B:ARG137
|
4.9
|
22.9
|
1.0
|
|
H
|
B:PHE166
|
4.9
|
28.0
|
1.0
|
|
HD2
|
B:HIS136
|
4.9
|
22.7
|
1.0
|
|
C
|
B:ARG137
|
4.9
|
25.1
|
1.0
|
|
CB
|
B:HIS136
|
5.0
|
24.0
|
1.0
|
|
Reference:
T.Battista,
M.S.Semrau,
G.Lolli,
P.Storici.
Crystal Structures of ULK1 in Complex with Kcgs Compounds To Be Published.
Page generated: Fri Oct 4 15:48:43 2024
|
