Chlorine in PDB 5ack: Human PDK1 Kinase Domain in Complex with Allosteric Compound 7 Bound to the Pif-Pocket
Enzymatic activity of Human PDK1 Kinase Domain in Complex with Allosteric Compound 7 Bound to the Pif-Pocket
All present enzymatic activity of Human PDK1 Kinase Domain in Complex with Allosteric Compound 7 Bound to the Pif-Pocket:
2.7.11.1;
Protein crystallography data
The structure of Human PDK1 Kinase Domain in Complex with Allosteric Compound 7 Bound to the Pif-Pocket, PDB code: 5ack
was solved by
J.O.Schulze,
E.Kroon,
A.Doemling,
R.M.Biondi,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
72.568 /
1.24
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
147.980,
44.540,
47.810,
90.00,
101.25,
90.00
|
R / Rfree (%)
|
14.16 /
16.55
|
Other elements in 5ack:
The structure of Human PDK1 Kinase Domain in Complex with Allosteric Compound 7 Bound to the Pif-Pocket also contains other interesting chemical elements:
Chlorine Binding Sites:
The binding sites of Chlorine atom in the Human PDK1 Kinase Domain in Complex with Allosteric Compound 7 Bound to the Pif-Pocket
(pdb code 5ack). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the
Human PDK1 Kinase Domain in Complex with Allosteric Compound 7 Bound to the Pif-Pocket, PDB code: 5ack:
Jump to Chlorine binding site number:
1;
2;
3;
4;
Chlorine binding site 1 out
of 4 in 5ack
Go back to
Chlorine Binding Sites List in 5ack
Chlorine binding site 1 out
of 4 in the Human PDK1 Kinase Domain in Complex with Allosteric Compound 7 Bound to the Pif-Pocket
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 1 of Human PDK1 Kinase Domain in Complex with Allosteric Compound 7 Bound to the Pif-Pocket within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl600
b:41.7
occ:0.53
|
CL2
|
A:SVQ600
|
0.0
|
41.7
|
0.5
|
C23
|
A:SVQ600
|
0.7
|
34.3
|
0.5
|
C22
|
A:SVQ600
|
1.4
|
34.8
|
0.5
|
C25
|
A:SVQ600
|
1.8
|
37.5
|
0.5
|
C24
|
A:SVQ600
|
2.0
|
34.7
|
0.5
|
HG13
|
A:VAL127
|
2.5
|
32.4
|
0.5
|
C21
|
A:SVQ600
|
2.6
|
35.5
|
0.5
|
C24
|
A:SVQ600
|
2.7
|
34.0
|
0.5
|
C20
|
A:SVQ600
|
2.9
|
35.9
|
0.5
|
C25
|
A:SVQ600
|
2.9
|
36.6
|
0.5
|
C20
|
A:SVQ600
|
3.1
|
36.1
|
0.5
|
HA
|
A:THR128
|
3.2
|
23.6
|
1.0
|
C14
|
A:SVQ600
|
3.3
|
37.2
|
0.5
|
HB2
|
A:ARG131
|
3.4
|
20.8
|
1.0
|
CG1
|
A:VAL127
|
3.4
|
27.0
|
0.5
|
HG21
|
A:VAL127
|
3.5
|
21.2
|
0.5
|
O
|
A:VAL127
|
3.5
|
19.9
|
1.0
|
HG12
|
A:VAL127
|
3.6
|
32.4
|
0.5
|
HB3
|
A:ARG131
|
3.7
|
20.8
|
1.0
|
HZ
|
A:PHE157
|
3.7
|
25.1
|
1.0
|
HG11
|
A:VAL127
|
3.8
|
32.4
|
0.5
|
C
|
A:VAL127
|
3.8
|
19.6
|
1.0
|
CD
|
A:ARG131
|
3.9
|
22.9
|
1.0
|
CB
|
A:ARG131
|
3.9
|
17.4
|
1.0
|
HB
|
A:VAL127
|
3.9
|
23.3
|
0.5
|
C23
|
A:SVQ600
|
4.0
|
32.1
|
0.5
|
CA
|
A:THR128
|
4.0
|
19.6
|
1.0
|
N
|
A:THR128
|
4.1
|
19.3
|
1.0
|
C21
|
A:SVQ600
|
4.1
|
34.1
|
0.5
|
C13
|
A:SVQ600
|
4.2
|
40.2
|
0.5
|
C8
|
A:SVQ600
|
4.2
|
33.5
|
0.5
|
C17
|
A:SVQ600
|
4.3
|
43.0
|
0.5
|
CG2
|
A:VAL127
|
4.3
|
17.7
|
0.5
|
HB
|
A:VAL127
|
4.3
|
30.2
|
0.5
|
CZ
|
A:PHE157
|
4.3
|
21.0
|
1.0
|
O19
|
A:SVQ600
|
4.3
|
43.9
|
0.5
|
HD23
|
A:LEU155
|
4.4
|
27.9
|
1.0
|
CB
|
A:VAL127
|
4.4
|
25.1
|
0.5
|
N9
|
A:SVQ600
|
4.4
|
35.6
|
0.5
|
HD11
|
A:LEU155
|
4.4
|
34.8
|
1.0
|
HG22
|
A:VAL127
|
4.5
|
21.2
|
0.5
|
CB
|
A:VAL127
|
4.5
|
19.4
|
0.5
|
CG
|
A:ARG131
|
4.5
|
19.6
|
1.0
|
CL2
|
A:SVQ600
|
4.5
|
37.6
|
0.5
|
C22
|
A:SVQ600
|
4.6
|
32.9
|
0.5
|
H
|
A:THR128
|
4.6
|
23.2
|
1.0
|
H
|
A:ARG131
|
4.6
|
19.5
|
1.0
|
C14
|
A:SVQ600
|
4.6
|
37.5
|
0.5
|
HG1
|
A:THR128
|
4.7
|
31.3
|
1.0
|
OG1
|
A:THR128
|
4.7
|
26.1
|
1.0
|
C1
|
A:SVQ600
|
4.7
|
30.3
|
0.5
|
CA
|
A:VAL127
|
4.7
|
21.0
|
0.5
|
O
|
A:HOH2061
|
4.8
|
40.1
|
1.0
|
CA
|
A:VAL127
|
4.8
|
19.2
|
0.5
|
O18
|
A:SVQ600
|
4.8
|
44.4
|
0.5
|
HE1
|
A:PHE157
|
4.8
|
25.4
|
1.0
|
HG21
|
A:THR128
|
4.8
|
29.7
|
1.0
|
C7
|
A:SVQ600
|
4.8
|
32.1
|
0.5
|
CE1
|
A:PHE157
|
4.9
|
21.2
|
1.0
|
C1
|
A:SVQ600
|
4.9
|
29.7
|
0.5
|
CB
|
A:THR128
|
5.0
|
23.4
|
1.0
|
HE2
|
A:PHE157
|
5.0
|
24.2
|
1.0
|
C
|
A:THR128
|
5.0
|
18.7
|
1.0
|
|
Chlorine binding site 2 out
of 4 in 5ack
Go back to
Chlorine Binding Sites List in 5ack
Chlorine binding site 2 out
of 4 in the Human PDK1 Kinase Domain in Complex with Allosteric Compound 7 Bound to the Pif-Pocket
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 2 of Human PDK1 Kinase Domain in Complex with Allosteric Compound 7 Bound to the Pif-Pocket within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl600
b:33.3
occ:0.53
|
CL1
|
A:SVQ600
|
0.0
|
33.3
|
0.5
|
CL1
|
A:SVQ600
|
0.6
|
34.9
|
0.5
|
C5
|
A:SVQ600
|
1.8
|
31.2
|
0.5
|
C5
|
A:SVQ600
|
2.2
|
32.2
|
0.5
|
C4
|
A:SVQ600
|
2.8
|
30.0
|
0.5
|
C6
|
A:SVQ600
|
2.8
|
29.9
|
0.5
|
HA
|
A:LYS115
|
2.9
|
31.2
|
1.0
|
HG13
|
A:ILE119
|
2.9
|
42.2
|
1.0
|
HB
|
A:ILE118
|
3.0
|
33.9
|
1.0
|
C6
|
A:SVQ600
|
3.0
|
30.5
|
0.5
|
HB3
|
A:LYS115
|
3.1
|
30.7
|
1.0
|
HG2
|
A:LYS115
|
3.1
|
30.6
|
1.0
|
C4
|
A:SVQ600
|
3.2
|
31.0
|
0.5
|
HG23
|
A:VAL124
|
3.2
|
33.5
|
1.0
|
HG22
|
A:ILE118
|
3.4
|
35.3
|
1.0
|
O
|
A:LYS115
|
3.4
|
29.8
|
1.0
|
HG23
|
A:ILE118
|
3.5
|
35.3
|
1.0
|
HD12
|
A:LEU155
|
3.5
|
34.8
|
1.0
|
HD12
|
A:ILE119
|
3.5
|
42.1
|
1.0
|
CA
|
A:LYS115
|
3.5
|
26.0
|
1.0
|
CB
|
A:LYS115
|
3.6
|
25.6
|
1.0
|
CG2
|
A:ILE118
|
3.7
|
29.4
|
1.0
|
CG1
|
A:ILE119
|
3.7
|
35.2
|
1.0
|
CB
|
A:ILE118
|
3.7
|
28.2
|
1.0
|
CG
|
A:LYS115
|
3.8
|
25.5
|
1.0
|
HD13
|
A:ILE119
|
3.8
|
42.1
|
1.0
|
C
|
A:LYS115
|
3.9
|
28.9
|
1.0
|
CD1
|
A:ILE119
|
3.9
|
35.1
|
1.0
|
H
|
A:ILE119
|
4.0
|
36.3
|
1.0
|
C3
|
A:SVQ600
|
4.0
|
29.6
|
0.5
|
C1
|
A:SVQ600
|
4.0
|
29.7
|
0.5
|
CG2
|
A:VAL124
|
4.1
|
27.9
|
1.0
|
HG12
|
A:ILE119
|
4.1
|
42.2
|
1.0
|
HG22
|
A:VAL124
|
4.2
|
33.5
|
1.0
|
C1
|
A:SVQ600
|
4.3
|
30.3
|
0.5
|
N
|
A:ILE119
|
4.3
|
30.2
|
1.0
|
CD1
|
A:LEU155
|
4.4
|
29.0
|
1.0
|
HG13
|
A:ILE118
|
4.4
|
35.5
|
1.0
|
HG21
|
A:VAL124
|
4.4
|
33.5
|
1.0
|
HD3
|
A:LYS115
|
4.5
|
30.9
|
1.0
|
C3
|
A:SVQ600
|
4.5
|
30.4
|
0.5
|
HB2
|
A:LYS115
|
4.5
|
30.7
|
1.0
|
HD13
|
A:LEU155
|
4.5
|
34.8
|
1.0
|
HG3
|
A:LYS115
|
4.5
|
30.6
|
1.0
|
C2
|
A:SVQ600
|
4.5
|
30.6
|
0.5
|
CG1
|
A:ILE118
|
4.6
|
29.6
|
1.0
|
HG21
|
A:ILE118
|
4.7
|
35.3
|
1.0
|
HE2
|
A:LYS115
|
4.7
|
32.3
|
1.0
|
CD
|
A:LYS115
|
4.7
|
25.7
|
1.0
|
HD22
|
A:LEU155
|
4.8
|
27.9
|
1.0
|
C
|
A:ILE118
|
4.8
|
29.8
|
1.0
|
HG11
|
A:VAL124
|
4.8
|
32.6
|
1.0
|
CA
|
A:ILE118
|
4.8
|
29.4
|
1.0
|
N
|
A:LYS115
|
4.8
|
24.8
|
1.0
|
HD11
|
A:ILE119
|
4.8
|
42.1
|
1.0
|
HG22
|
A:VAL127
|
4.8
|
21.2
|
0.5
|
HG12
|
A:ILE118
|
4.9
|
35.5
|
1.0
|
CB
|
A:ILE119
|
4.9
|
34.4
|
1.0
|
HG
|
A:LEU155
|
4.9
|
28.8
|
1.0
|
HA
|
A:ILE119
|
4.9
|
39.7
|
1.0
|
C2
|
A:SVQ600
|
4.9
|
30.9
|
0.5
|
H
|
A:ILE118
|
4.9
|
37.0
|
1.0
|
HA
|
A:VAL124
|
4.9
|
29.3
|
1.0
|
HD11
|
A:LEU155
|
5.0
|
34.8
|
1.0
|
|
Chlorine binding site 3 out
of 4 in 5ack
Go back to
Chlorine Binding Sites List in 5ack
Chlorine binding site 3 out
of 4 in the Human PDK1 Kinase Domain in Complex with Allosteric Compound 7 Bound to the Pif-Pocket
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 3 of Human PDK1 Kinase Domain in Complex with Allosteric Compound 7 Bound to the Pif-Pocket within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl600
b:37.6
occ:0.47
|
CL2
|
A:SVQ600
|
0.0
|
37.6
|
0.5
|
C22
|
A:SVQ600
|
0.8
|
32.9
|
0.5
|
C23
|
A:SVQ600
|
0.9
|
32.1
|
0.5
|
C25
|
A:SVQ600
|
1.8
|
36.6
|
0.5
|
C21
|
A:SVQ600
|
2.1
|
34.1
|
0.5
|
C24
|
A:SVQ600
|
2.1
|
34.0
|
0.5
|
C24
|
A:SVQ600
|
2.7
|
34.7
|
0.5
|
C25
|
A:SVQ600
|
2.8
|
37.5
|
0.5
|
C20
|
A:SVQ600
|
2.8
|
35.9
|
0.5
|
C20
|
A:SVQ600
|
2.8
|
36.1
|
0.5
|
HB
|
A:THR148
|
2.9
|
23.9
|
1.0
|
HD23
|
A:LEU155
|
3.1
|
27.9
|
1.0
|
O
|
A:PHE149
|
3.1
|
19.9
|
1.0
|
C14
|
A:SVQ600
|
3.2
|
37.5
|
0.5
|
HB3
|
A:LEU155
|
3.3
|
25.3
|
1.0
|
HB3
|
A:GLN150
|
3.3
|
29.4
|
1.0
|
H
|
A:TYR156
|
3.4
|
19.9
|
1.0
|
HD21
|
A:LEU155
|
3.6
|
27.9
|
1.0
|
H
|
A:PHE149
|
3.6
|
23.1
|
1.0
|
C
|
A:PHE149
|
3.7
|
19.5
|
1.0
|
HA
|
A:LEU155
|
3.7
|
23.1
|
1.0
|
CD2
|
A:LEU155
|
3.8
|
23.2
|
1.0
|
C17
|
A:SVQ600
|
3.8
|
42.4
|
0.5
|
C13
|
A:SVQ600
|
3.8
|
40.3
|
0.5
|
CB
|
A:THR148
|
3.9
|
19.9
|
1.0
|
N
|
A:PHE149
|
3.9
|
19.2
|
1.0
|
O19
|
A:SVQ600
|
4.0
|
42.0
|
0.5
|
C23
|
A:SVQ600
|
4.0
|
34.3
|
0.5
|
O
|
A:TYR156
|
4.0
|
16.0
|
1.0
|
CB
|
A:LEU155
|
4.1
|
21.1
|
1.0
|
N
|
A:TYR156
|
4.1
|
16.5
|
1.0
|
C21
|
A:SVQ600
|
4.1
|
35.5
|
0.5
|
HA
|
A:PHE149
|
4.2
|
24.2
|
1.0
|
CA
|
A:PHE149
|
4.2
|
20.2
|
1.0
|
C14
|
A:SVQ600
|
4.3
|
37.2
|
0.5
|
HG1
|
A:THR148
|
4.3
|
27.3
|
1.0
|
CB
|
A:GLN150
|
4.3
|
24.5
|
1.0
|
O18
|
A:SVQ600
|
4.3
|
43.5
|
0.5
|
CA
|
A:LEU155
|
4.3
|
19.3
|
1.0
|
OG1
|
A:THR148
|
4.4
|
22.8
|
1.0
|
N
|
A:GLN150
|
4.4
|
22.0
|
1.0
|
N9
|
A:SVQ600
|
4.4
|
36.2
|
0.5
|
HD22
|
A:LEU155
|
4.5
|
27.9
|
1.0
|
C
|
A:THR148
|
4.5
|
19.8
|
1.0
|
HG22
|
A:THR148
|
4.5
|
24.7
|
1.0
|
CL2
|
A:SVQ600
|
4.5
|
41.7
|
0.5
|
C8
|
A:SVQ600
|
4.5
|
33.6
|
0.5
|
CG
|
A:LEU155
|
4.6
|
24.0
|
1.0
|
C22
|
A:SVQ600
|
4.6
|
34.8
|
0.5
|
HA
|
A:GLN150
|
4.6
|
27.7
|
1.0
|
CG2
|
A:THR148
|
4.6
|
20.6
|
1.0
|
C
|
A:LEU155
|
4.7
|
17.2
|
1.0
|
N9
|
A:SVQ600
|
4.7
|
35.6
|
0.5
|
CA
|
A:THR148
|
4.7
|
18.5
|
1.0
|
HG23
|
A:THR148
|
4.7
|
24.7
|
1.0
|
CA
|
A:GLN150
|
4.7
|
23.1
|
1.0
|
C8
|
A:SVQ600
|
4.8
|
33.5
|
0.5
|
HA
|
A:THR148
|
4.8
|
22.2
|
1.0
|
C
|
A:TYR156
|
4.8
|
15.7
|
1.0
|
HB2
|
A:GLN150
|
4.8
|
29.4
|
1.0
|
HG2
|
A:GLN150
|
4.8
|
33.3
|
1.0
|
HB2
|
A:LEU155
|
4.9
|
25.3
|
1.0
|
C13
|
A:SVQ600
|
4.9
|
40.2
|
0.5
|
HD11
|
A:LEU155
|
5.0
|
34.8
|
1.0
|
|
Chlorine binding site 4 out
of 4 in 5ack
Go back to
Chlorine Binding Sites List in 5ack
Chlorine binding site 4 out
of 4 in the Human PDK1 Kinase Domain in Complex with Allosteric Compound 7 Bound to the Pif-Pocket
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 4 of Human PDK1 Kinase Domain in Complex with Allosteric Compound 7 Bound to the Pif-Pocket within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl600
b:34.9
occ:0.47
|
CL1
|
A:SVQ600
|
0.0
|
34.9
|
0.5
|
CL1
|
A:SVQ600
|
0.6
|
33.3
|
0.5
|
C5
|
A:SVQ600
|
1.4
|
31.2
|
0.5
|
C5
|
A:SVQ600
|
1.8
|
32.2
|
0.5
|
C4
|
A:SVQ600
|
2.3
|
30.0
|
0.5
|
C6
|
A:SVQ600
|
2.6
|
29.9
|
0.5
|
C4
|
A:SVQ600
|
2.7
|
31.0
|
0.5
|
C6
|
A:SVQ600
|
2.8
|
30.5
|
0.5
|
HG13
|
A:ILE119
|
3.0
|
42.2
|
1.0
|
HB3
|
A:LYS115
|
3.1
|
30.7
|
1.0
|
HG23
|
A:VAL124
|
3.2
|
33.5
|
1.0
|
HG2
|
A:LYS115
|
3.2
|
30.6
|
1.0
|
HD12
|
A:ILE119
|
3.2
|
42.1
|
1.0
|
HA
|
A:LYS115
|
3.4
|
31.2
|
1.0
|
HB
|
A:ILE118
|
3.6
|
33.9
|
1.0
|
C3
|
A:SVQ600
|
3.6
|
29.6
|
0.5
|
HD12
|
A:LEU155
|
3.7
|
34.8
|
1.0
|
CG1
|
A:ILE119
|
3.7
|
35.2
|
1.0
|
C1
|
A:SVQ600
|
3.8
|
29.7
|
0.5
|
CB
|
A:LYS115
|
3.8
|
25.6
|
1.0
|
CD1
|
A:ILE119
|
3.8
|
35.1
|
1.0
|
HG22
|
A:ILE118
|
3.8
|
35.3
|
1.0
|
O
|
A:LYS115
|
3.8
|
29.8
|
1.0
|
HD13
|
A:ILE119
|
3.8
|
42.1
|
1.0
|
HG23
|
A:ILE118
|
3.9
|
35.3
|
1.0
|
CG
|
A:LYS115
|
3.9
|
25.5
|
1.0
|
CA
|
A:LYS115
|
3.9
|
26.0
|
1.0
|
HG12
|
A:ILE119
|
4.0
|
42.2
|
1.0
|
C3
|
A:SVQ600
|
4.0
|
30.4
|
0.5
|
CG2
|
A:VAL124
|
4.0
|
27.9
|
1.0
|
C1
|
A:SVQ600
|
4.0
|
30.3
|
0.5
|
HG22
|
A:VAL124
|
4.0
|
33.5
|
1.0
|
C2
|
A:SVQ600
|
4.1
|
30.6
|
0.5
|
CG2
|
A:ILE118
|
4.2
|
29.4
|
1.0
|
C
|
A:LYS115
|
4.3
|
28.9
|
1.0
|
HD3
|
A:LYS115
|
4.3
|
30.9
|
1.0
|
CB
|
A:ILE118
|
4.3
|
28.2
|
1.0
|
H
|
A:ILE119
|
4.4
|
36.3
|
1.0
|
HG21
|
A:VAL124
|
4.5
|
33.5
|
1.0
|
HE2
|
A:LYS115
|
4.5
|
32.3
|
1.0
|
C2
|
A:SVQ600
|
4.6
|
30.9
|
0.5
|
HG11
|
A:VAL124
|
4.6
|
32.6
|
1.0
|
CD1
|
A:LEU155
|
4.6
|
29.0
|
1.0
|
CD
|
A:LYS115
|
4.6
|
25.7
|
1.0
|
HB2
|
A:LYS115
|
4.7
|
30.7
|
1.0
|
HD11
|
A:ILE119
|
4.7
|
42.1
|
1.0
|
HG3
|
A:LYS115
|
4.7
|
30.6
|
1.0
|
HD22
|
A:LEU155
|
4.7
|
27.9
|
1.0
|
N
|
A:ILE119
|
4.7
|
30.2
|
1.0
|
HD13
|
A:LEU155
|
4.8
|
34.8
|
1.0
|
HG13
|
A:ILE118
|
4.9
|
35.5
|
1.0
|
CB
|
A:ILE119
|
5.0
|
34.4
|
1.0
|
|
Reference:
E.Kroon,
J.O.Schulze,
E.Suss,
C.J.Camacho,
R.M.Biondi,
A.Domling.
Discovery of A Potent Allosteric Kinase Modulator By Combining Computational and Synthetic Methods. Angew.Chem.Int.Ed.Engl. V. 54 13933 2015.
ISSN: ISSN 1433-7851
PubMed: 26385475
DOI: 10.1002/ANIE.201506310
Page generated: Fri Jul 26 05:06:19 2024
|