Bromine in PDB 1p5e: The Structure of Phospho-CDK2/Cyclin A in Complex with the Inhibitor 4,5,6,7-Tetrabromobenzotriazole (Tbs)
Protein crystallography data
The structure of The Structure of Phospho-CDK2/Cyclin A in Complex with the Inhibitor 4,5,6,7-Tetrabromobenzotriazole (Tbs), PDB code: 1p5e
was solved by
E.De Moliner,
N.R.Brown,
L.N.Johnson,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
46.97 /
2.22
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
73.536,
133.947,
148.424,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
21.9 /
25.7
|
Bromine Binding Sites:
The binding sites of Bromine atom in the The Structure of Phospho-CDK2/Cyclin A in Complex with the Inhibitor 4,5,6,7-Tetrabromobenzotriazole (Tbs)
(pdb code 1p5e). This binding sites where shown within
5.0 Angstroms radius around Bromine atom.
In total 8 binding sites of Bromine where determined in the
The Structure of Phospho-CDK2/Cyclin A in Complex with the Inhibitor 4,5,6,7-Tetrabromobenzotriazole (Tbs), PDB code: 1p5e:
Jump to Bromine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Bromine binding site 1 out
of 8 in 1p5e
Go back to
Bromine Binding Sites List in 1p5e
Bromine binding site 1 out
of 8 in the The Structure of Phospho-CDK2/Cyclin A in Complex with the Inhibitor 4,5,6,7-Tetrabromobenzotriazole (Tbs)
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 1 of The Structure of Phospho-CDK2/Cyclin A in Complex with the Inhibitor 4,5,6,7-Tetrabromobenzotriazole (Tbs) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Br301
b:65.6
occ:1.00
|
BR10
|
A:TBS301
|
0.0
|
65.6
|
1.0
|
C4
|
A:TBS301
|
1.9
|
59.2
|
1.0
|
C6
|
A:TBS301
|
2.8
|
59.0
|
1.0
|
C1
|
A:TBS301
|
2.8
|
56.1
|
1.0
|
O
|
A:HOH325
|
3.0
|
34.5
|
1.0
|
O
|
A:ILE10
|
3.2
|
33.2
|
1.0
|
N5
|
A:TBS301
|
3.3
|
59.0
|
1.0
|
BR11
|
A:TBS301
|
3.3
|
57.4
|
1.0
|
CD1
|
A:ILE10
|
3.8
|
30.3
|
1.0
|
C
|
A:ILE10
|
3.8
|
33.2
|
1.0
|
CG1
|
A:ILE10
|
4.0
|
31.2
|
1.0
|
CB
|
A:ILE10
|
4.1
|
32.3
|
1.0
|
C2
|
A:TBS301
|
4.1
|
54.2
|
1.0
|
C7
|
A:TBS301
|
4.1
|
58.6
|
1.0
|
N
|
A:GLY11
|
4.4
|
33.9
|
1.0
|
CA
|
A:GLY11
|
4.5
|
35.0
|
1.0
|
C3
|
A:TBS301
|
4.6
|
56.7
|
1.0
|
CA
|
A:ILE10
|
4.6
|
32.5
|
1.0
|
N9
|
A:TBS301
|
4.6
|
59.2
|
1.0
|
CD2
|
A:LEU134
|
4.9
|
19.2
|
1.0
|
CG1
|
A:VAL18
|
4.9
|
32.2
|
1.0
|
|
Bromine binding site 2 out
of 8 in 1p5e
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Bromine Binding Sites List in 1p5e
Bromine binding site 2 out
of 8 in the The Structure of Phospho-CDK2/Cyclin A in Complex with the Inhibitor 4,5,6,7-Tetrabromobenzotriazole (Tbs)
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 2 of The Structure of Phospho-CDK2/Cyclin A in Complex with the Inhibitor 4,5,6,7-Tetrabromobenzotriazole (Tbs) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Br301
b:57.4
occ:1.00
|
BR11
|
A:TBS301
|
0.0
|
57.4
|
1.0
|
C1
|
A:TBS301
|
1.9
|
56.1
|
1.0
|
C2
|
A:TBS301
|
2.8
|
54.2
|
1.0
|
C4
|
A:TBS301
|
2.9
|
59.2
|
1.0
|
O
|
A:LEU83
|
2.9
|
25.6
|
1.0
|
BR12
|
A:TBS301
|
3.1
|
40.2
|
1.0
|
BR10
|
A:TBS301
|
3.3
|
65.6
|
1.0
|
CD1
|
A:ILE10
|
3.5
|
30.3
|
1.0
|
N
|
A:LEU83
|
3.8
|
24.4
|
1.0
|
C
|
A:LEU83
|
3.8
|
25.5
|
1.0
|
C3
|
A:TBS301
|
4.0
|
56.7
|
1.0
|
CD1
|
A:LEU134
|
4.1
|
20.0
|
1.0
|
C6
|
A:TBS301
|
4.2
|
59.0
|
1.0
|
CA
|
A:LEU83
|
4.2
|
25.0
|
1.0
|
O
|
A:HOH325
|
4.2
|
34.5
|
1.0
|
CB
|
A:LEU83
|
4.2
|
25.1
|
1.0
|
CD1
|
A:PHE82
|
4.3
|
24.5
|
1.0
|
CE1
|
A:PHE82
|
4.3
|
24.8
|
1.0
|
CB
|
A:ALA31
|
4.5
|
23.8
|
1.0
|
C7
|
A:TBS301
|
4.6
|
58.6
|
1.0
|
CG1
|
A:ILE10
|
4.8
|
31.2
|
1.0
|
CD2
|
A:LEU134
|
4.8
|
19.2
|
1.0
|
C
|
A:PHE82
|
4.9
|
24.2
|
1.0
|
N
|
A:HIS84
|
5.0
|
26.1
|
1.0
|
|
Bromine binding site 3 out
of 8 in 1p5e
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Bromine Binding Sites List in 1p5e
Bromine binding site 3 out
of 8 in the The Structure of Phospho-CDK2/Cyclin A in Complex with the Inhibitor 4,5,6,7-Tetrabromobenzotriazole (Tbs)
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 3 of The Structure of Phospho-CDK2/Cyclin A in Complex with the Inhibitor 4,5,6,7-Tetrabromobenzotriazole (Tbs) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Br301
b:40.2
occ:1.00
|
BR12
|
A:TBS301
|
0.0
|
40.2
|
1.0
|
C2
|
A:TBS301
|
1.9
|
54.2
|
1.0
|
C1
|
A:TBS301
|
2.8
|
56.1
|
1.0
|
C3
|
A:TBS301
|
2.9
|
56.7
|
1.0
|
O
|
A:GLU81
|
3.0
|
23.5
|
1.0
|
BR11
|
A:TBS301
|
3.1
|
57.4
|
1.0
|
BR13
|
A:TBS301
|
3.2
|
63.7
|
1.0
|
CB
|
A:ALA31
|
3.5
|
23.8
|
1.0
|
CD1
|
A:LEU134
|
3.7
|
20.0
|
1.0
|
N
|
A:LEU83
|
3.9
|
24.4
|
1.0
|
CG2
|
A:VAL64
|
4.0
|
21.3
|
1.0
|
CB
|
A:PHE80
|
4.1
|
23.6
|
1.0
|
C4
|
A:TBS301
|
4.1
|
59.2
|
1.0
|
C
|
A:GLU81
|
4.2
|
23.8
|
1.0
|
C7
|
A:TBS301
|
4.2
|
58.6
|
1.0
|
CD1
|
A:LEU83
|
4.3
|
25.4
|
1.0
|
CB
|
A:LEU83
|
4.4
|
25.1
|
1.0
|
CA
|
A:PHE82
|
4.4
|
24.0
|
1.0
|
CG
|
A:LEU83
|
4.5
|
24.8
|
1.0
|
C
|
A:PHE82
|
4.6
|
24.2
|
1.0
|
C6
|
A:TBS301
|
4.7
|
59.0
|
1.0
|
N
|
A:PHE82
|
4.8
|
23.9
|
1.0
|
CA
|
A:LEU83
|
4.8
|
25.0
|
1.0
|
CG
|
A:PHE80
|
4.8
|
24.0
|
1.0
|
CA
|
A:ALA31
|
4.9
|
24.4
|
1.0
|
O
|
A:LEU83
|
5.0
|
25.6
|
1.0
|
|
Bromine binding site 4 out
of 8 in 1p5e
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Bromine Binding Sites List in 1p5e
Bromine binding site 4 out
of 8 in the The Structure of Phospho-CDK2/Cyclin A in Complex with the Inhibitor 4,5,6,7-Tetrabromobenzotriazole (Tbs)
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 4 of The Structure of Phospho-CDK2/Cyclin A in Complex with the Inhibitor 4,5,6,7-Tetrabromobenzotriazole (Tbs) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Br301
b:63.7
occ:1.00
|
BR13
|
A:TBS301
|
0.0
|
63.7
|
1.0
|
C3
|
A:TBS301
|
1.9
|
56.7
|
1.0
|
C2
|
A:TBS301
|
2.8
|
54.2
|
1.0
|
C7
|
A:TBS301
|
2.8
|
58.6
|
1.0
|
O
|
A:HOH302
|
2.9
|
23.4
|
1.0
|
BR12
|
A:TBS301
|
3.2
|
40.2
|
1.0
|
CD2
|
A:PHE80
|
3.3
|
24.3
|
1.0
|
N8
|
A:TBS301
|
3.3
|
58.8
|
1.0
|
CG
|
A:PHE80
|
3.4
|
24.0
|
1.0
|
CE2
|
A:PHE80
|
3.7
|
24.0
|
1.0
|
CB
|
A:PHE80
|
3.8
|
23.6
|
1.0
|
CD1
|
A:PHE80
|
3.8
|
23.9
|
1.0
|
CG2
|
A:VAL64
|
4.0
|
21.3
|
1.0
|
C1
|
A:TBS301
|
4.0
|
56.1
|
1.0
|
O
|
A:HOH399
|
4.0
|
47.2
|
1.0
|
CZ
|
A:PHE80
|
4.1
|
23.0
|
1.0
|
C6
|
A:TBS301
|
4.1
|
59.0
|
1.0
|
CE1
|
A:PHE80
|
4.2
|
23.7
|
1.0
|
CD1
|
A:LEU134
|
4.5
|
20.0
|
1.0
|
C4
|
A:TBS301
|
4.6
|
59.2
|
1.0
|
CG1
|
A:VAL64
|
4.6
|
19.5
|
1.0
|
N9
|
A:TBS301
|
4.6
|
59.2
|
1.0
|
CB
|
A:ALA31
|
4.8
|
23.8
|
1.0
|
CB
|
A:ALA144
|
4.8
|
17.8
|
1.0
|
CB
|
A:VAL64
|
4.9
|
19.4
|
1.0
|
|
Bromine binding site 5 out
of 8 in 1p5e
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Bromine Binding Sites List in 1p5e
Bromine binding site 5 out
of 8 in the The Structure of Phospho-CDK2/Cyclin A in Complex with the Inhibitor 4,5,6,7-Tetrabromobenzotriazole (Tbs)
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 5 of The Structure of Phospho-CDK2/Cyclin A in Complex with the Inhibitor 4,5,6,7-Tetrabromobenzotriazole (Tbs) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Br302
b:78.1
occ:1.00
|
BR10
|
C:TBS302
|
0.0
|
78.1
|
1.0
|
C4
|
C:TBS302
|
1.9
|
72.1
|
1.0
|
C6
|
C:TBS302
|
2.8
|
72.2
|
1.0
|
C1
|
C:TBS302
|
2.9
|
69.0
|
1.0
|
O
|
C:HOH338
|
3.0
|
47.0
|
1.0
|
N5
|
C:TBS302
|
3.2
|
72.6
|
1.0
|
BR11
|
C:TBS302
|
3.4
|
69.9
|
1.0
|
O
|
C:ILE10
|
3.8
|
47.0
|
1.0
|
C7
|
C:TBS302
|
4.1
|
71.5
|
1.0
|
C2
|
C:TBS302
|
4.2
|
66.7
|
1.0
|
CD1
|
C:ILE10
|
4.3
|
43.3
|
1.0
|
CB
|
C:ILE10
|
4.4
|
45.3
|
1.0
|
CG1
|
C:ILE10
|
4.5
|
44.9
|
1.0
|
CD2
|
C:LEU134
|
4.5
|
29.9
|
1.0
|
N9
|
C:TBS302
|
4.6
|
73.1
|
1.0
|
C
|
C:ILE10
|
4.6
|
46.9
|
1.0
|
C3
|
C:TBS302
|
4.6
|
69.0
|
1.0
|
OD2
|
C:ASP86
|
5.0
|
39.1
|
1.0
|
|
Bromine binding site 6 out
of 8 in 1p5e
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Bromine Binding Sites List in 1p5e
Bromine binding site 6 out
of 8 in the The Structure of Phospho-CDK2/Cyclin A in Complex with the Inhibitor 4,5,6,7-Tetrabromobenzotriazole (Tbs)
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 6 of The Structure of Phospho-CDK2/Cyclin A in Complex with the Inhibitor 4,5,6,7-Tetrabromobenzotriazole (Tbs) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Br302
b:69.9
occ:1.00
|
BR11
|
C:TBS302
|
0.0
|
69.9
|
1.0
|
C1
|
C:TBS302
|
1.9
|
69.0
|
1.0
|
C2
|
C:TBS302
|
2.8
|
66.7
|
1.0
|
O
|
C:LEU83
|
2.9
|
35.2
|
1.0
|
C4
|
C:TBS302
|
2.9
|
72.1
|
1.0
|
BR12
|
C:TBS302
|
3.3
|
53.0
|
1.0
|
BR10
|
C:TBS302
|
3.4
|
78.1
|
1.0
|
N
|
C:LEU83
|
3.7
|
32.5
|
1.0
|
C
|
C:LEU83
|
3.7
|
34.9
|
1.0
|
CA
|
C:LEU83
|
4.0
|
34.0
|
1.0
|
CD1
|
C:LEU134
|
4.1
|
31.5
|
1.0
|
C3
|
C:TBS302
|
4.1
|
69.0
|
1.0
|
CD1
|
C:ILE10
|
4.2
|
43.3
|
1.0
|
C6
|
C:TBS302
|
4.2
|
72.2
|
1.0
|
CB
|
C:LEU83
|
4.2
|
34.0
|
1.0
|
CE1
|
C:PHE82
|
4.3
|
34.2
|
1.0
|
CD1
|
C:PHE82
|
4.3
|
33.3
|
1.0
|
CD2
|
C:LEU134
|
4.5
|
29.9
|
1.0
|
C7
|
C:TBS302
|
4.7
|
71.5
|
1.0
|
N
|
C:HIS84
|
4.7
|
35.9
|
1.0
|
CG
|
C:LEU134
|
4.8
|
30.4
|
1.0
|
C
|
C:PHE82
|
4.8
|
31.5
|
1.0
|
CB
|
C:ALA31
|
5.0
|
27.4
|
1.0
|
|
Bromine binding site 7 out
of 8 in 1p5e
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Bromine Binding Sites List in 1p5e
Bromine binding site 7 out
of 8 in the The Structure of Phospho-CDK2/Cyclin A in Complex with the Inhibitor 4,5,6,7-Tetrabromobenzotriazole (Tbs)
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 7 of The Structure of Phospho-CDK2/Cyclin A in Complex with the Inhibitor 4,5,6,7-Tetrabromobenzotriazole (Tbs) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Br302
b:53.0
occ:1.00
|
BR12
|
C:TBS302
|
0.0
|
53.0
|
1.0
|
C2
|
C:TBS302
|
1.9
|
66.7
|
1.0
|
C3
|
C:TBS302
|
2.8
|
69.0
|
1.0
|
C1
|
C:TBS302
|
2.9
|
69.0
|
1.0
|
O
|
C:GLU81
|
3.0
|
27.0
|
1.0
|
BR13
|
C:TBS302
|
3.2
|
72.7
|
1.0
|
BR11
|
C:TBS302
|
3.3
|
69.9
|
1.0
|
CB
|
C:ALA31
|
3.6
|
27.4
|
1.0
|
CD1
|
C:LEU134
|
3.6
|
31.5
|
1.0
|
N
|
C:LEU83
|
4.0
|
32.5
|
1.0
|
CB
|
C:PHE80
|
4.1
|
23.7
|
1.0
|
C7
|
C:TBS302
|
4.2
|
71.5
|
1.0
|
C
|
C:GLU81
|
4.2
|
27.8
|
1.0
|
C4
|
C:TBS302
|
4.2
|
72.1
|
1.0
|
CG2
|
C:VAL64
|
4.2
|
27.6
|
1.0
|
CA
|
C:PHE82
|
4.3
|
30.8
|
1.0
|
C
|
C:PHE82
|
4.6
|
31.5
|
1.0
|
C6
|
C:TBS302
|
4.7
|
72.2
|
1.0
|
CD1
|
C:LEU83
|
4.7
|
34.6
|
1.0
|
N
|
C:PHE82
|
4.7
|
29.3
|
1.0
|
CB
|
C:LEU83
|
4.8
|
34.0
|
1.0
|
CG
|
C:PHE80
|
4.8
|
22.4
|
1.0
|
CA
|
C:LEU83
|
4.9
|
34.0
|
1.0
|
CA
|
C:ALA31
|
5.0
|
27.5
|
1.0
|
CG
|
C:LEU83
|
5.0
|
33.9
|
1.0
|
|
Bromine binding site 8 out
of 8 in 1p5e
Go back to
Bromine Binding Sites List in 1p5e
Bromine binding site 8 out
of 8 in the The Structure of Phospho-CDK2/Cyclin A in Complex with the Inhibitor 4,5,6,7-Tetrabromobenzotriazole (Tbs)
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 8 of The Structure of Phospho-CDK2/Cyclin A in Complex with the Inhibitor 4,5,6,7-Tetrabromobenzotriazole (Tbs) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Br302
b:72.7
occ:1.00
|
BR13
|
C:TBS302
|
0.0
|
72.7
|
1.0
|
C3
|
C:TBS302
|
1.9
|
69.0
|
1.0
|
C2
|
C:TBS302
|
2.8
|
66.7
|
1.0
|
C7
|
C:TBS302
|
2.8
|
71.5
|
1.0
|
O
|
C:HOH303
|
3.0
|
24.9
|
1.0
|
BR12
|
C:TBS302
|
3.2
|
53.0
|
1.0
|
CD2
|
C:PHE80
|
3.2
|
21.7
|
1.0
|
N8
|
C:TBS302
|
3.3
|
72.2
|
1.0
|
CG
|
C:PHE80
|
3.4
|
22.4
|
1.0
|
O
|
C:HOH305
|
3.6
|
37.9
|
1.0
|
CB
|
C:PHE80
|
3.7
|
23.7
|
1.0
|
CE2
|
C:PHE80
|
3.8
|
20.7
|
1.0
|
CD1
|
C:PHE80
|
4.1
|
21.6
|
1.0
|
C1
|
C:TBS302
|
4.1
|
69.0
|
1.0
|
C6
|
C:TBS302
|
4.2
|
72.2
|
1.0
|
CZ
|
C:PHE80
|
4.4
|
20.4
|
1.0
|
CB
|
C:ALA31
|
4.4
|
27.4
|
1.0
|
CE1
|
C:PHE80
|
4.5
|
20.9
|
1.0
|
CG2
|
C:VAL64
|
4.6
|
27.6
|
1.0
|
C4
|
C:TBS302
|
4.6
|
72.1
|
1.0
|
N9
|
C:TBS302
|
4.7
|
73.1
|
1.0
|
CG1
|
C:VAL18
|
4.7
|
45.2
|
1.0
|
CD1
|
C:LEU134
|
4.8
|
31.5
|
1.0
|
CD
|
C:LYS33
|
4.9
|
30.6
|
1.0
|
|
Reference:
E.De Moliner,
N.R.Brown,
L.N.Johnson.
Alternative Binding Modes of An Inhibitor to Two Different Kinases Eur.J.Biochem. V. 270 1 2003.
ISSN: ISSN 0014-2956
PubMed: 12869192
DOI: 10.1046/J.1432-1033.2003.03697.X
Page generated: Wed Jul 10 17:13:30 2024
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