Chlorine in PDB 5iez: Discovery of Potent Myeloid Cell Leukemia-1 (Mcl-1) Inhibitors Using Structure-Based Design
Protein crystallography data
The structure of Discovery of Potent Myeloid Cell Leukemia-1 (Mcl-1) Inhibitors Using Structure-Based Design, PDB code: 5iez
was solved by
B.Zhao,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.84 /
2.60
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
39.914,
136.046,
63.499,
90.00,
101.62,
90.00
|
R / Rfree (%)
|
19.4 /
27.7
|
Chlorine Binding Sites:
The binding sites of Chlorine atom in the Discovery of Potent Myeloid Cell Leukemia-1 (Mcl-1) Inhibitors Using Structure-Based Design
(pdb code 5iez). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the
Discovery of Potent Myeloid Cell Leukemia-1 (Mcl-1) Inhibitors Using Structure-Based Design, PDB code: 5iez:
Jump to Chlorine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Chlorine binding site 1 out
of 8 in 5iez
Go back to
Chlorine Binding Sites List in 5iez
Chlorine binding site 1 out
of 8 in the Discovery of Potent Myeloid Cell Leukemia-1 (Mcl-1) Inhibitors Using Structure-Based Design
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 1 of Discovery of Potent Myeloid Cell Leukemia-1 (Mcl-1) Inhibitors Using Structure-Based Design within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl400
b:38.6
occ:1.00
|
CL
|
A:6AL400
|
0.0
|
38.6
|
1.0
|
C02
|
A:6AL400
|
1.8
|
37.0
|
1.0
|
C03
|
A:6AL400
|
2.7
|
33.1
|
1.0
|
C35
|
A:6AL400
|
2.8
|
42.4
|
1.0
|
O
|
A:ALA227
|
3.1
|
36.2
|
1.0
|
C36
|
A:6AL400
|
3.2
|
43.1
|
1.0
|
CB
|
A:MET231
|
3.3
|
37.8
|
1.0
|
C
|
A:ALA227
|
3.6
|
33.8
|
1.0
|
CD1
|
A:PHE228
|
3.6
|
29.0
|
1.0
|
O
|
A:HOH502
|
3.6
|
37.6
|
1.0
|
C37
|
A:6AL400
|
3.7
|
52.8
|
1.0
|
CG
|
A:MET231
|
3.8
|
41.1
|
1.0
|
N
|
A:PHE228
|
4.0
|
33.0
|
1.0
|
CA
|
A:PHE228
|
4.0
|
30.2
|
1.0
|
C42
|
A:6AL400
|
4.0
|
26.7
|
1.0
|
C04
|
A:6AL400
|
4.0
|
28.9
|
1.0
|
C38
|
A:6AL400
|
4.1
|
57.7
|
1.0
|
C06
|
A:6AL400
|
4.1
|
41.5
|
1.0
|
CB
|
A:ALA227
|
4.1
|
37.0
|
1.0
|
CE1
|
A:PHE228
|
4.1
|
35.8
|
1.0
|
CA
|
A:ALA227
|
4.4
|
36.3
|
1.0
|
CE1
|
A:PHE270
|
4.5
|
26.7
|
1.0
|
C43
|
A:6AL400
|
4.6
|
21.8
|
1.0
|
C05
|
A:6AL400
|
4.6
|
36.7
|
1.0
|
N39
|
A:6AL400
|
4.6
|
49.1
|
1.0
|
CA
|
A:MET231
|
4.6
|
33.9
|
1.0
|
CZ
|
A:PHE270
|
4.7
|
29.6
|
1.0
|
CG
|
A:PHE228
|
4.7
|
28.4
|
1.0
|
N41
|
A:6AL400
|
4.7
|
34.5
|
1.0
|
CD1
|
A:PHE270
|
4.7
|
21.9
|
1.0
|
N
|
A:MET231
|
4.7
|
34.5
|
1.0
|
CE
|
A:MET231
|
4.9
|
58.6
|
1.0
|
C
|
A:PHE228
|
4.9
|
30.7
|
1.0
|
CB
|
A:PHE228
|
4.9
|
29.0
|
1.0
|
|
Chlorine binding site 2 out
of 8 in 5iez
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Chlorine Binding Sites List in 5iez
Chlorine binding site 2 out
of 8 in the Discovery of Potent Myeloid Cell Leukemia-1 (Mcl-1) Inhibitors Using Structure-Based Design
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 2 of Discovery of Potent Myeloid Cell Leukemia-1 (Mcl-1) Inhibitors Using Structure-Based Design within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl400
b:50.0
occ:1.00
|
CL2
|
A:6AL400
|
0.0
|
50.0
|
1.0
|
C33
|
A:6AL400
|
1.8
|
42.6
|
1.0
|
C31
|
A:6AL400
|
2.7
|
34.5
|
1.0
|
C28
|
A:6AL400
|
2.7
|
24.4
|
1.0
|
C29
|
A:6AL400
|
2.9
|
15.4
|
1.0
|
C32
|
A:6AL400
|
3.0
|
40.1
|
1.0
|
CE2
|
A:PHE270
|
3.5
|
27.0
|
1.0
|
CD2
|
A:PHE270
|
3.8
|
22.4
|
1.0
|
CD1
|
A:LEU235
|
4.0
|
30.9
|
1.0
|
C30
|
A:6AL400
|
4.0
|
35.2
|
1.0
|
CG2
|
A:VAL274
|
4.0
|
21.0
|
1.0
|
C27
|
A:6AL400
|
4.0
|
28.5
|
1.0
|
C26
|
A:6AL400
|
4.5
|
35.7
|
1.0
|
CB
|
A:MET250
|
4.6
|
34.6
|
1.0
|
CZ
|
A:PHE270
|
4.7
|
29.6
|
1.0
|
CD2
|
A:LEU246
|
4.7
|
45.2
|
1.0
|
CD1
|
A:LEU246
|
4.8
|
52.6
|
1.0
|
CB
|
A:LEU246
|
4.9
|
43.3
|
1.0
|
CB
|
A:VAL274
|
4.9
|
20.3
|
1.0
|
|
Chlorine binding site 3 out
of 8 in 5iez
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Chlorine Binding Sites List in 5iez
Chlorine binding site 3 out
of 8 in the Discovery of Potent Myeloid Cell Leukemia-1 (Mcl-1) Inhibitors Using Structure-Based Design
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 3 of Discovery of Potent Myeloid Cell Leukemia-1 (Mcl-1) Inhibitors Using Structure-Based Design within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl400
b:38.7
occ:1.00
|
CL
|
B:6AL400
|
0.0
|
38.7
|
1.0
|
C02
|
B:6AL400
|
1.8
|
41.5
|
1.0
|
C35
|
B:6AL400
|
2.7
|
34.6
|
1.0
|
C03
|
B:6AL400
|
2.8
|
40.6
|
1.0
|
O
|
B:ALA227
|
3.0
|
31.1
|
1.0
|
C36
|
B:6AL400
|
3.1
|
45.4
|
1.0
|
C
|
B:ALA227
|
3.4
|
28.4
|
1.0
|
CD1
|
B:PHE228
|
3.4
|
44.6
|
1.0
|
CB
|
B:MET231
|
3.7
|
44.7
|
1.0
|
C37
|
B:6AL400
|
3.7
|
50.1
|
1.0
|
C42
|
B:6AL400
|
3.7
|
43.7
|
1.0
|
N
|
B:PHE228
|
3.8
|
26.0
|
1.0
|
CA
|
B:PHE228
|
3.8
|
30.4
|
1.0
|
CB
|
B:ALA227
|
3.9
|
34.7
|
1.0
|
CE1
|
B:PHE228
|
4.0
|
40.0
|
1.0
|
C06
|
B:6AL400
|
4.0
|
36.9
|
1.0
|
C04
|
B:6AL400
|
4.1
|
42.3
|
1.0
|
C38
|
B:6AL400
|
4.2
|
53.5
|
1.0
|
C43
|
B:6AL400
|
4.2
|
42.5
|
1.0
|
CA
|
B:ALA227
|
4.2
|
26.9
|
1.0
|
SD
|
B:MET231
|
4.4
|
53.5
|
1.0
|
CG
|
B:MET231
|
4.4
|
49.2
|
1.0
|
N39
|
B:6AL400
|
4.5
|
47.1
|
1.0
|
N41
|
B:6AL400
|
4.5
|
47.2
|
1.0
|
CG
|
B:PHE228
|
4.6
|
25.2
|
1.0
|
C05
|
B:6AL400
|
4.6
|
45.1
|
1.0
|
CE2
|
B:PHE270
|
4.8
|
25.2
|
1.0
|
C
|
B:PHE228
|
4.8
|
26.4
|
1.0
|
CB
|
B:PHE228
|
4.8
|
25.8
|
1.0
|
N
|
B:MET231
|
4.8
|
37.3
|
1.0
|
CZ
|
B:PHE270
|
4.9
|
24.8
|
1.0
|
CA
|
B:MET231
|
4.9
|
38.2
|
1.0
|
O
|
B:PHE228
|
5.0
|
26.2
|
1.0
|
CD2
|
B:PHE270
|
5.0
|
29.6
|
1.0
|
|
Chlorine binding site 4 out
of 8 in 5iez
Go back to
Chlorine Binding Sites List in 5iez
Chlorine binding site 4 out
of 8 in the Discovery of Potent Myeloid Cell Leukemia-1 (Mcl-1) Inhibitors Using Structure-Based Design
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 4 of Discovery of Potent Myeloid Cell Leukemia-1 (Mcl-1) Inhibitors Using Structure-Based Design within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl400
b:34.5
occ:1.00
|
CL2
|
B:6AL400
|
0.0
|
34.5
|
1.0
|
C33
|
B:6AL400
|
1.8
|
35.5
|
1.0
|
C31
|
B:6AL400
|
2.7
|
37.4
|
1.0
|
C28
|
B:6AL400
|
2.8
|
23.8
|
1.0
|
C32
|
B:6AL400
|
3.0
|
35.2
|
1.0
|
C29
|
B:6AL400
|
3.1
|
7.0
|
1.0
|
CD2
|
B:LEU246
|
3.8
|
50.9
|
1.0
|
C30
|
B:6AL400
|
4.0
|
36.9
|
1.0
|
CE1
|
B:PHE270
|
4.0
|
31.1
|
1.0
|
C27
|
B:6AL400
|
4.0
|
24.4
|
1.0
|
CD1
|
B:PHE270
|
4.2
|
35.0
|
1.0
|
CB
|
B:LEU246
|
4.5
|
33.9
|
1.0
|
CD1
|
B:LEU235
|
4.5
|
42.4
|
1.0
|
C26
|
B:6AL400
|
4.5
|
29.1
|
1.0
|
O
|
B:LEU246
|
4.6
|
29.2
|
1.0
|
CG
|
B:LEU246
|
4.6
|
44.6
|
1.0
|
CB
|
B:MET250
|
4.7
|
35.2
|
1.0
|
CG2
|
B:VAL274
|
4.7
|
20.1
|
1.0
|
CD1
|
B:LEU246
|
4.8
|
42.5
|
1.0
|
CD1
|
B:LEU290
|
4.8
|
36.8
|
1.0
|
C
|
B:LEU246
|
4.9
|
28.3
|
1.0
|
CG
|
B:MET250
|
5.0
|
42.0
|
1.0
|
|
Chlorine binding site 5 out
of 8 in 5iez
Go back to
Chlorine Binding Sites List in 5iez
Chlorine binding site 5 out
of 8 in the Discovery of Potent Myeloid Cell Leukemia-1 (Mcl-1) Inhibitors Using Structure-Based Design
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 5 of Discovery of Potent Myeloid Cell Leukemia-1 (Mcl-1) Inhibitors Using Structure-Based Design within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cl400
b:32.9
occ:1.00
|
CL
|
C:6AL400
|
0.0
|
32.9
|
1.0
|
C02
|
C:6AL400
|
1.8
|
36.9
|
1.0
|
C03
|
C:6AL400
|
2.7
|
42.2
|
1.0
|
C35
|
C:6AL400
|
2.8
|
40.3
|
1.0
|
O
|
C:ALA227
|
2.9
|
38.2
|
1.0
|
CB
|
C:MET231
|
3.2
|
35.4
|
1.0
|
C36
|
C:6AL400
|
3.2
|
44.1
|
1.0
|
C
|
C:ALA227
|
3.4
|
40.0
|
1.0
|
CD1
|
C:PHE228
|
3.4
|
44.5
|
1.0
|
CG
|
C:MET231
|
3.7
|
48.3
|
1.0
|
C37
|
C:6AL400
|
3.8
|
41.6
|
1.0
|
N
|
C:PHE228
|
3.8
|
40.3
|
1.0
|
CA
|
C:PHE228
|
3.8
|
42.9
|
1.0
|
CE1
|
C:PHE228
|
4.0
|
36.4
|
1.0
|
C42
|
C:6AL400
|
4.0
|
44.7
|
1.0
|
C04
|
C:6AL400
|
4.0
|
42.4
|
1.0
|
C06
|
C:6AL400
|
4.0
|
39.2
|
1.0
|
CB
|
C:ALA227
|
4.1
|
40.2
|
1.0
|
C38
|
C:6AL400
|
4.1
|
31.7
|
1.0
|
CA
|
C:ALA227
|
4.3
|
40.7
|
1.0
|
CA
|
C:MET231
|
4.5
|
36.5
|
1.0
|
CG
|
C:PHE228
|
4.5
|
39.2
|
1.0
|
CE
|
C:MET231
|
4.5
|
51.7
|
1.0
|
C05
|
C:6AL400
|
4.6
|
41.5
|
1.0
|
C43
|
C:6AL400
|
4.6
|
46.5
|
1.0
|
N39
|
C:6AL400
|
4.6
|
50.6
|
1.0
|
N
|
C:MET231
|
4.6
|
41.4
|
1.0
|
CE1
|
C:PHE270
|
4.6
|
33.7
|
1.0
|
CD1
|
C:PHE270
|
4.7
|
39.1
|
1.0
|
N41
|
C:6AL400
|
4.7
|
47.1
|
1.0
|
C
|
C:PHE228
|
4.8
|
43.5
|
1.0
|
CB
|
C:PHE228
|
4.8
|
36.4
|
1.0
|
O
|
C:PHE228
|
4.9
|
36.5
|
1.0
|
SD
|
C:MET231
|
4.9
|
50.2
|
1.0
|
|
Chlorine binding site 6 out
of 8 in 5iez
Go back to
Chlorine Binding Sites List in 5iez
Chlorine binding site 6 out
of 8 in the Discovery of Potent Myeloid Cell Leukemia-1 (Mcl-1) Inhibitors Using Structure-Based Design
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 6 of Discovery of Potent Myeloid Cell Leukemia-1 (Mcl-1) Inhibitors Using Structure-Based Design within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cl400
b:41.5
occ:1.00
|
CL2
|
C:6AL400
|
0.0
|
41.5
|
1.0
|
C33
|
C:6AL400
|
1.7
|
45.5
|
1.0
|
C28
|
C:6AL400
|
2.7
|
51.8
|
1.0
|
C31
|
C:6AL400
|
2.7
|
43.6
|
1.0
|
C29
|
C:6AL400
|
2.9
|
54.0
|
1.0
|
C32
|
C:6AL400
|
3.1
|
34.4
|
1.0
|
CD1
|
C:LEU246
|
3.6
|
30.6
|
1.0
|
CD2
|
C:LEU246
|
3.8
|
31.5
|
1.0
|
CE2
|
C:PHE270
|
3.8
|
35.1
|
1.0
|
CE
|
C:MET250
|
3.8
|
35.3
|
1.0
|
C27
|
C:6AL400
|
4.0
|
50.4
|
1.0
|
CD1
|
C:LEU235
|
4.0
|
32.3
|
1.0
|
CG
|
C:LEU246
|
4.0
|
31.0
|
1.0
|
C30
|
C:6AL400
|
4.0
|
48.2
|
1.0
|
CB
|
C:LEU246
|
4.0
|
30.6
|
1.0
|
CD2
|
C:PHE270
|
4.2
|
29.7
|
1.0
|
C26
|
C:6AL400
|
4.5
|
45.0
|
1.0
|
CG2
|
C:VAL274
|
4.5
|
28.6
|
1.0
|
CD1
|
C:LEU290
|
4.8
|
24.4
|
1.0
|
CB
|
C:MET250
|
4.9
|
33.9
|
1.0
|
O
|
C:LEU246
|
4.9
|
30.7
|
1.0
|
CZ
|
C:PHE270
|
4.9
|
30.2
|
1.0
|
|
Chlorine binding site 7 out
of 8 in 5iez
Go back to
Chlorine Binding Sites List in 5iez
Chlorine binding site 7 out
of 8 in the Discovery of Potent Myeloid Cell Leukemia-1 (Mcl-1) Inhibitors Using Structure-Based Design
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 7 of Discovery of Potent Myeloid Cell Leukemia-1 (Mcl-1) Inhibitors Using Structure-Based Design within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Cl400
b:75.0
occ:1.00
|
CL
|
D:6AL400
|
0.0
|
75.0
|
1.0
|
C02
|
D:6AL400
|
1.8
|
47.6
|
1.0
|
C03
|
D:6AL400
|
2.7
|
38.5
|
1.0
|
C35
|
D:6AL400
|
2.8
|
34.9
|
1.0
|
O
|
D:ALA227
|
3.2
|
47.3
|
1.0
|
C36
|
D:6AL400
|
3.2
|
33.4
|
1.0
|
CD1
|
D:PHE228
|
3.3
|
29.7
|
1.0
|
CB
|
D:MET231
|
3.4
|
36.0
|
1.0
|
C
|
D:ALA227
|
3.5
|
40.7
|
1.0
|
C37
|
D:6AL400
|
3.8
|
45.0
|
1.0
|
CE1
|
D:PHE228
|
3.8
|
30.8
|
1.0
|
N
|
D:PHE228
|
3.8
|
37.8
|
1.0
|
CB
|
D:ALA227
|
3.9
|
28.3
|
1.0
|
CA
|
D:PHE228
|
3.9
|
39.8
|
1.0
|
CG
|
D:MET231
|
3.9
|
39.2
|
1.0
|
C42
|
D:6AL400
|
3.9
|
31.4
|
1.0
|
C04
|
D:6AL400
|
4.1
|
27.4
|
1.0
|
C06
|
D:6AL400
|
4.1
|
33.3
|
1.0
|
C38
|
D:6AL400
|
4.2
|
45.4
|
1.0
|
CA
|
D:ALA227
|
4.2
|
43.6
|
1.0
|
CG
|
D:PHE228
|
4.4
|
32.6
|
1.0
|
C43
|
D:6AL400
|
4.5
|
31.5
|
1.0
|
CE1
|
D:PHE270
|
4.6
|
31.8
|
1.0
|
N39
|
D:6AL400
|
4.6
|
49.8
|
1.0
|
CD1
|
D:PHE270
|
4.6
|
40.3
|
1.0
|
C05
|
D:6AL400
|
4.6
|
23.9
|
1.0
|
CE
|
D:MET231
|
4.6
|
44.9
|
1.0
|
N41
|
D:6AL400
|
4.7
|
45.1
|
1.0
|
CB
|
D:PHE228
|
4.8
|
34.2
|
1.0
|
CA
|
D:MET231
|
4.8
|
40.5
|
1.0
|
N
|
D:MET231
|
4.9
|
44.8
|
1.0
|
C
|
D:PHE228
|
4.9
|
47.7
|
1.0
|
CZ
|
D:PHE270
|
4.9
|
28.6
|
1.0
|
|
Chlorine binding site 8 out
of 8 in 5iez
Go back to
Chlorine Binding Sites List in 5iez
Chlorine binding site 8 out
of 8 in the Discovery of Potent Myeloid Cell Leukemia-1 (Mcl-1) Inhibitors Using Structure-Based Design
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 8 of Discovery of Potent Myeloid Cell Leukemia-1 (Mcl-1) Inhibitors Using Structure-Based Design within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Cl400
b:36.5
occ:1.00
|
CL2
|
D:6AL400
|
0.0
|
36.5
|
1.0
|
C33
|
D:6AL400
|
1.8
|
38.6
|
1.0
|
C31
|
D:6AL400
|
2.7
|
41.3
|
1.0
|
C28
|
D:6AL400
|
2.8
|
36.9
|
1.0
|
C32
|
D:6AL400
|
3.1
|
48.8
|
1.0
|
C29
|
D:6AL400
|
3.1
|
21.9
|
1.0
|
CD2
|
D:LEU246
|
3.6
|
28.1
|
1.0
|
CE
|
D:MET250
|
3.7
|
40.4
|
1.0
|
CD1
|
D:LEU246
|
3.7
|
36.5
|
1.0
|
CG
|
D:LEU246
|
4.0
|
29.2
|
1.0
|
C30
|
D:6AL400
|
4.0
|
46.4
|
1.0
|
CB
|
D:LEU246
|
4.1
|
29.7
|
1.0
|
C27
|
D:6AL400
|
4.1
|
37.4
|
1.0
|
CE2
|
D:PHE270
|
4.2
|
34.3
|
1.0
|
CD2
|
D:PHE270
|
4.4
|
32.7
|
1.0
|
CD1
|
D:LEU235
|
4.5
|
26.0
|
1.0
|
CG2
|
D:VAL274
|
4.6
|
26.7
|
1.0
|
C26
|
D:6AL400
|
4.6
|
44.0
|
1.0
|
CB
|
D:MET250
|
4.8
|
30.5
|
1.0
|
CD1
|
D:LEU290
|
4.8
|
28.2
|
1.0
|
CG
|
D:MET250
|
4.9
|
38.4
|
1.0
|
O
|
D:LEU246
|
5.0
|
35.9
|
1.0
|
|
Reference:
T.Lee,
Z.Bian,
B.Zhao,
L.J.Hogdal,
J.L.Sensintaffar,
C.M.Goodwin,
J.Belmar,
S.Shaw,
J.C.Tarr,
N.Veerasamy,
S.M.Matulis,
B.Koss,
M.A.Fischer,
A.L.Arnold,
D.V.Camper,
C.F.Browning,
O.W.Rossanese,
A.Budhraja,
J.Opferman,
L.H.Boise,
M.R.Savona,
A.Letai,
E.T.Olejniczak,
S.W.Fesik.
Discovery and Biological Characterization of Potent Myeloid Cell Leukemia-1 Inhibitors. Febs Lett. V. 591 240 2017.
ISSN: ISSN 1873-3468
PubMed: 27878989
DOI: 10.1002/1873-3468.12497
Page generated: Fri Jul 26 09:16:26 2024
|