Chlorine in PDB 6e6e: Dgy-06-116, A Novel and Selective Covalent Inhibitor of Src Kinase
Enzymatic activity of Dgy-06-116, A Novel and Selective Covalent Inhibitor of Src Kinase
All present enzymatic activity of Dgy-06-116, A Novel and Selective Covalent Inhibitor of Src Kinase:
2.7.10.2;
Protein crystallography data
The structure of Dgy-06-116, A Novel and Selective Covalent Inhibitor of Src Kinase, PDB code: 6e6e
was solved by
D.Gurbani,
A.Bera,
K.Westover,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
43.66 /
2.15
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
63.534,
84.028,
120.109,
89.96,
90.05,
90.12
|
R / Rfree (%)
|
25 /
28.5
|
Chlorine Binding Sites:
The binding sites of Chlorine atom in the Dgy-06-116, A Novel and Selective Covalent Inhibitor of Src Kinase
(pdb code 6e6e). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the
Dgy-06-116, A Novel and Selective Covalent Inhibitor of Src Kinase, PDB code: 6e6e:
Jump to Chlorine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Chlorine binding site 1 out
of 8 in 6e6e
Go back to
Chlorine Binding Sites List in 6e6e
Chlorine binding site 1 out
of 8 in the Dgy-06-116, A Novel and Selective Covalent Inhibitor of Src Kinase
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 1 of Dgy-06-116, A Novel and Selective Covalent Inhibitor of Src Kinase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl601
b:56.4
occ:1.00
|
CL1
|
A:HVY601
|
0.0
|
56.4
|
1.0
|
C30
|
A:HVY601
|
1.7
|
50.9
|
1.0
|
C29
|
A:HVY601
|
2.7
|
46.2
|
1.0
|
C25
|
A:HVY601
|
2.7
|
45.9
|
1.0
|
N9
|
A:HVY601
|
3.0
|
45.3
|
1.0
|
C24
|
A:HVY601
|
3.2
|
42.0
|
1.0
|
O3
|
A:HVY601
|
3.2
|
41.4
|
1.0
|
CG1
|
A:VAL323
|
3.5
|
33.5
|
1.0
|
O
|
A:HOH701
|
3.5
|
46.9
|
1.0
|
CB
|
A:ALA403
|
3.5
|
29.8
|
1.0
|
CD1
|
A:LEU393
|
3.6
|
33.9
|
1.0
|
CB
|
A:VAL323
|
3.7
|
42.2
|
1.0
|
CG2
|
A:VAL323
|
3.7
|
33.3
|
1.0
|
C28
|
A:HVY601
|
4.0
|
46.1
|
1.0
|
C26
|
A:HVY601
|
4.0
|
47.1
|
1.0
|
C13
|
A:HVY601
|
4.2
|
38.1
|
1.0
|
CA
|
A:ALA403
|
4.5
|
32.6
|
1.0
|
C27
|
A:HVY601
|
4.5
|
46.7
|
1.0
|
C22
|
A:HVY601
|
4.5
|
42.8
|
1.0
|
OG1
|
A:THR338
|
4.6
|
41.4
|
1.0
|
N
|
A:ASP404
|
4.8
|
40.7
|
1.0
|
C12
|
A:HVY601
|
4.8
|
41.3
|
1.0
|
CG
|
A:LEU393
|
4.8
|
31.1
|
1.0
|
|
Chlorine binding site 2 out
of 8 in 6e6e
Go back to
Chlorine Binding Sites List in 6e6e
Chlorine binding site 2 out
of 8 in the Dgy-06-116, A Novel and Selective Covalent Inhibitor of Src Kinase
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 2 of Dgy-06-116, A Novel and Selective Covalent Inhibitor of Src Kinase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl601
b:54.4
occ:1.00
|
CL1
|
B:HVY601
|
0.0
|
54.4
|
1.0
|
C30
|
B:HVY601
|
1.7
|
51.1
|
1.0
|
C29
|
B:HVY601
|
2.7
|
44.4
|
1.0
|
C25
|
B:HVY601
|
2.7
|
46.4
|
1.0
|
N9
|
B:HVY601
|
3.0
|
41.4
|
1.0
|
C24
|
B:HVY601
|
3.3
|
43.2
|
1.0
|
O3
|
B:HVY601
|
3.3
|
43.6
|
1.0
|
CG1
|
B:VAL323
|
3.4
|
39.5
|
1.0
|
CB
|
B:ALA403
|
3.5
|
36.7
|
1.0
|
CB
|
B:VAL323
|
3.7
|
40.7
|
1.0
|
O
|
B:HOH709
|
3.7
|
49.7
|
1.0
|
CG2
|
B:VAL323
|
3.8
|
34.7
|
1.0
|
CD1
|
B:LEU393
|
3.8
|
35.6
|
1.0
|
C28
|
B:HVY601
|
4.0
|
44.1
|
1.0
|
C26
|
B:HVY601
|
4.0
|
49.2
|
1.0
|
C13
|
B:HVY601
|
4.2
|
38.3
|
1.0
|
CA
|
B:ALA403
|
4.3
|
35.5
|
1.0
|
C27
|
B:HVY601
|
4.5
|
48.2
|
1.0
|
N
|
B:ASP404
|
4.6
|
44.0
|
1.0
|
OG1
|
B:THR338
|
4.6
|
43.1
|
1.0
|
C12
|
B:HVY601
|
4.7
|
38.0
|
1.0
|
C22
|
B:HVY601
|
4.9
|
42.8
|
1.0
|
C23
|
B:HVY601
|
4.9
|
56.2
|
1.0
|
CG
|
B:LEU393
|
5.0
|
33.2
|
1.0
|
|
Chlorine binding site 3 out
of 8 in 6e6e
Go back to
Chlorine Binding Sites List in 6e6e
Chlorine binding site 3 out
of 8 in the Dgy-06-116, A Novel and Selective Covalent Inhibitor of Src Kinase
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 3 of Dgy-06-116, A Novel and Selective Covalent Inhibitor of Src Kinase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cl601
b:52.8
occ:1.00
|
CL1
|
C:HVY601
|
0.0
|
52.8
|
1.0
|
C30
|
C:HVY601
|
1.7
|
48.0
|
1.0
|
C29
|
C:HVY601
|
2.7
|
47.1
|
1.0
|
C25
|
C:HVY601
|
2.7
|
42.5
|
1.0
|
N9
|
C:HVY601
|
3.0
|
38.6
|
1.0
|
C24
|
C:HVY601
|
3.2
|
40.2
|
1.0
|
O3
|
C:HVY601
|
3.3
|
41.9
|
1.0
|
CB
|
C:ALA403
|
3.5
|
35.2
|
1.0
|
CG1
|
C:VAL323
|
3.5
|
36.2
|
1.0
|
CD1
|
C:LEU393
|
3.6
|
36.4
|
1.0
|
CB
|
C:VAL323
|
3.8
|
37.8
|
1.0
|
CG2
|
C:VAL323
|
4.0
|
33.1
|
1.0
|
C28
|
C:HVY601
|
4.0
|
46.8
|
1.0
|
C26
|
C:HVY601
|
4.0
|
42.3
|
1.0
|
O
|
C:HOH722
|
4.1
|
46.9
|
1.0
|
C13
|
C:HVY601
|
4.2
|
38.9
|
1.0
|
CA
|
C:ALA403
|
4.5
|
39.7
|
1.0
|
C27
|
C:HVY601
|
4.5
|
43.3
|
1.0
|
OG1
|
C:THR338
|
4.6
|
43.8
|
1.0
|
C22
|
C:HVY601
|
4.7
|
39.2
|
1.0
|
C12
|
C:HVY601
|
4.8
|
37.1
|
1.0
|
N
|
C:ASP404
|
4.8
|
44.3
|
1.0
|
CG
|
C:LEU393
|
4.8
|
33.2
|
1.0
|
|
Chlorine binding site 4 out
of 8 in 6e6e
Go back to
Chlorine Binding Sites List in 6e6e
Chlorine binding site 4 out
of 8 in the Dgy-06-116, A Novel and Selective Covalent Inhibitor of Src Kinase
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 4 of Dgy-06-116, A Novel and Selective Covalent Inhibitor of Src Kinase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Cl601
b:55.0
occ:1.00
|
CL1
|
D:HVY601
|
0.0
|
55.0
|
1.0
|
C30
|
D:HVY601
|
1.7
|
49.6
|
1.0
|
C29
|
D:HVY601
|
2.7
|
50.6
|
1.0
|
C25
|
D:HVY601
|
2.7
|
39.8
|
1.0
|
N9
|
D:HVY601
|
3.0
|
33.1
|
1.0
|
C24
|
D:HVY601
|
3.2
|
39.1
|
1.0
|
O3
|
D:HVY601
|
3.3
|
42.3
|
1.0
|
CG1
|
D:VAL323
|
3.5
|
40.1
|
1.0
|
CB
|
D:ALA403
|
3.5
|
39.7
|
1.0
|
CD1
|
D:LEU393
|
3.7
|
33.1
|
1.0
|
CB
|
D:VAL323
|
3.8
|
38.9
|
1.0
|
CG2
|
D:VAL323
|
3.9
|
36.6
|
1.0
|
C28
|
D:HVY601
|
4.0
|
49.7
|
1.0
|
C26
|
D:HVY601
|
4.0
|
47.8
|
1.0
|
C13
|
D:HVY601
|
4.2
|
40.3
|
1.0
|
CA
|
D:ALA403
|
4.4
|
44.2
|
1.0
|
C27
|
D:HVY601
|
4.5
|
49.0
|
1.0
|
OG1
|
D:THR338
|
4.6
|
41.4
|
1.0
|
N
|
D:ASP404
|
4.6
|
45.5
|
1.0
|
C22
|
D:HVY601
|
4.8
|
44.4
|
1.0
|
C12
|
D:HVY601
|
4.8
|
38.9
|
1.0
|
CG
|
D:LEU393
|
5.0
|
29.8
|
1.0
|
|
Chlorine binding site 5 out
of 8 in 6e6e
Go back to
Chlorine Binding Sites List in 6e6e
Chlorine binding site 5 out
of 8 in the Dgy-06-116, A Novel and Selective Covalent Inhibitor of Src Kinase
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 5 of Dgy-06-116, A Novel and Selective Covalent Inhibitor of Src Kinase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Cl601
b:53.4
occ:1.00
|
CL1
|
E:HVY601
|
0.0
|
53.4
|
1.0
|
C30
|
E:HVY601
|
1.7
|
47.4
|
1.0
|
C29
|
E:HVY601
|
2.7
|
42.6
|
1.0
|
C25
|
E:HVY601
|
2.7
|
44.8
|
1.0
|
N9
|
E:HVY601
|
2.9
|
44.1
|
1.0
|
O
|
E:ALA293
|
3.3
|
48.3
|
1.0
|
OG1
|
E:THR338
|
3.4
|
46.1
|
1.0
|
C24
|
E:HVY601
|
3.5
|
44.1
|
1.0
|
N
|
E:LYS295
|
3.5
|
46.8
|
1.0
|
O
|
E:ILE336
|
3.6
|
48.1
|
1.0
|
CB
|
E:LYS295
|
3.7
|
50.9
|
1.0
|
C
|
E:ALA293
|
3.7
|
45.0
|
1.0
|
O3
|
E:HVY601
|
3.8
|
41.5
|
1.0
|
C
|
E:ILE294
|
4.0
|
48.3
|
1.0
|
C28
|
E:HVY601
|
4.0
|
46.4
|
1.0
|
C26
|
E:HVY601
|
4.0
|
44.9
|
1.0
|
CB
|
E:ALA293
|
4.0
|
41.9
|
1.0
|
N
|
E:ILE294
|
4.1
|
49.4
|
1.0
|
CA
|
E:LYS295
|
4.1
|
53.9
|
1.0
|
CA
|
E:ILE294
|
4.2
|
43.8
|
1.0
|
CG2
|
E:THR338
|
4.2
|
47.8
|
1.0
|
C13
|
E:HVY601
|
4.3
|
40.9
|
1.0
|
N
|
E:THR338
|
4.3
|
51.9
|
1.0
|
CB
|
E:THR338
|
4.4
|
44.9
|
1.0
|
CG1
|
E:VAL281
|
4.4
|
46.8
|
1.0
|
O
|
E:HOH711
|
4.5
|
48.8
|
1.0
|
C27
|
E:HVY601
|
4.5
|
50.2
|
1.0
|
CA
|
E:ALA293
|
4.5
|
47.6
|
1.0
|
C
|
E:ILE336
|
4.6
|
48.6
|
1.0
|
C12
|
E:HVY601
|
4.6
|
45.6
|
1.0
|
O
|
E:ILE294
|
4.8
|
49.0
|
1.0
|
CA
|
E:THR338
|
4.9
|
50.2
|
1.0
|
CA
|
E:VAL337
|
5.0
|
50.2
|
1.0
|
C
|
E:VAL337
|
5.0
|
50.7
|
1.0
|
|
Chlorine binding site 6 out
of 8 in 6e6e
Go back to
Chlorine Binding Sites List in 6e6e
Chlorine binding site 6 out
of 8 in the Dgy-06-116, A Novel and Selective Covalent Inhibitor of Src Kinase
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 6 of Dgy-06-116, A Novel and Selective Covalent Inhibitor of Src Kinase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Cl601
b:56.8
occ:1.00
|
CL1
|
F:HVY601
|
0.0
|
56.8
|
1.0
|
C30
|
F:HVY601
|
1.7
|
46.1
|
1.0
|
C29
|
F:HVY601
|
2.7
|
46.3
|
1.0
|
C25
|
F:HVY601
|
2.7
|
45.0
|
1.0
|
N9
|
F:HVY601
|
3.0
|
41.3
|
1.0
|
O3
|
F:HVY601
|
3.2
|
35.6
|
1.0
|
C24
|
F:HVY601
|
3.2
|
41.2
|
1.0
|
CD1
|
F:LEU393
|
3.5
|
26.4
|
1.0
|
CG1
|
F:VAL323
|
3.6
|
34.0
|
1.0
|
CB
|
F:ALA403
|
3.6
|
37.6
|
1.0
|
CG2
|
F:VAL323
|
3.8
|
32.2
|
1.0
|
O
|
F:HOH711
|
3.8
|
42.1
|
1.0
|
CB
|
F:VAL323
|
3.8
|
40.1
|
1.0
|
C28
|
F:HVY601
|
4.0
|
44.2
|
1.0
|
C26
|
F:HVY601
|
4.0
|
41.2
|
1.0
|
C13
|
F:HVY601
|
4.2
|
39.7
|
1.0
|
C23
|
F:HVY601
|
4.3
|
59.5
|
1.0
|
C22
|
F:HVY601
|
4.4
|
48.1
|
1.0
|
C27
|
F:HVY601
|
4.5
|
44.6
|
1.0
|
OG1
|
F:THR338
|
4.6
|
45.2
|
1.0
|
CA
|
F:ALA403
|
4.6
|
41.7
|
1.0
|
CG
|
F:LEU393
|
4.8
|
34.0
|
1.0
|
C12
|
F:HVY601
|
4.8
|
42.6
|
1.0
|
N
|
F:ASP404
|
4.9
|
45.1
|
1.0
|
|
Chlorine binding site 7 out
of 8 in 6e6e
Go back to
Chlorine Binding Sites List in 6e6e
Chlorine binding site 7 out
of 8 in the Dgy-06-116, A Novel and Selective Covalent Inhibitor of Src Kinase
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 7 of Dgy-06-116, A Novel and Selective Covalent Inhibitor of Src Kinase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Cl601
b:58.9
occ:1.00
|
CL1
|
G:HVY601
|
0.0
|
58.9
|
1.0
|
C30
|
G:HVY601
|
1.7
|
38.4
|
1.0
|
C25
|
G:HVY601
|
2.7
|
39.4
|
1.0
|
C29
|
G:HVY601
|
2.7
|
47.8
|
1.0
|
N9
|
G:HVY601
|
2.9
|
37.4
|
1.0
|
OG1
|
G:THR338
|
3.3
|
47.0
|
1.0
|
C24
|
G:HVY601
|
3.5
|
40.5
|
1.0
|
O
|
G:ALA293
|
3.5
|
45.0
|
1.0
|
CB
|
G:LYS295
|
3.6
|
52.8
|
1.0
|
C
|
G:ALA293
|
3.7
|
47.8
|
1.0
|
O
|
G:ILE336
|
3.8
|
54.4
|
1.0
|
O3
|
G:HVY601
|
3.8
|
40.9
|
1.0
|
CB
|
G:ALA293
|
3.8
|
46.0
|
1.0
|
N
|
G:LYS295
|
3.8
|
49.8
|
1.0
|
C
|
G:ILE294
|
4.0
|
51.6
|
1.0
|
C28
|
G:HVY601
|
4.0
|
50.2
|
1.0
|
C26
|
G:HVY601
|
4.0
|
43.1
|
1.0
|
N
|
G:ILE294
|
4.1
|
41.5
|
1.0
|
CG2
|
G:THR338
|
4.2
|
46.6
|
1.0
|
CA
|
G:LYS295
|
4.2
|
49.7
|
1.0
|
C13
|
G:HVY601
|
4.3
|
44.6
|
1.0
|
CA
|
G:ILE294
|
4.3
|
49.3
|
1.0
|
CB
|
G:THR338
|
4.3
|
46.7
|
1.0
|
CG1
|
G:VAL281
|
4.3
|
44.6
|
1.0
|
CA
|
G:ALA293
|
4.4
|
52.5
|
1.0
|
N
|
G:THR338
|
4.4
|
54.4
|
1.0
|
O
|
G:ILE294
|
4.5
|
50.6
|
1.0
|
C27
|
G:HVY601
|
4.5
|
49.5
|
1.0
|
C12
|
G:HVY601
|
4.5
|
42.2
|
1.0
|
O
|
G:HOH704
|
4.5
|
47.1
|
1.0
|
CG
|
G:LYS295
|
4.6
|
58.3
|
1.0
|
C
|
G:ILE336
|
4.7
|
54.4
|
1.0
|
CD
|
G:LYS295
|
4.9
|
51.9
|
1.0
|
CA
|
G:THR338
|
5.0
|
51.1
|
1.0
|
CG2
|
G:VAL281
|
5.0
|
49.0
|
1.0
|
|
Chlorine binding site 8 out
of 8 in 6e6e
Go back to
Chlorine Binding Sites List in 6e6e
Chlorine binding site 8 out
of 8 in the Dgy-06-116, A Novel and Selective Covalent Inhibitor of Src Kinase
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 8 of Dgy-06-116, A Novel and Selective Covalent Inhibitor of Src Kinase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Cl601
b:60.1
occ:1.00
|
CL1
|
H:HVY601
|
0.0
|
60.1
|
1.0
|
C30
|
H:HVY601
|
1.7
|
49.5
|
1.0
|
C29
|
H:HVY601
|
2.7
|
49.5
|
1.0
|
C25
|
H:HVY601
|
2.7
|
47.9
|
1.0
|
N9
|
H:HVY601
|
3.0
|
41.5
|
1.0
|
O3
|
H:HVY601
|
3.2
|
37.6
|
1.0
|
C24
|
H:HVY601
|
3.2
|
38.1
|
1.0
|
CD1
|
H:LEU393
|
3.4
|
29.8
|
1.0
|
O
|
H:HOH706
|
3.5
|
46.1
|
1.0
|
CG1
|
H:VAL323
|
3.6
|
32.1
|
1.0
|
CB
|
H:ALA403
|
3.6
|
34.8
|
1.0
|
CB
|
H:VAL323
|
3.9
|
45.7
|
1.0
|
CG2
|
H:VAL323
|
3.9
|
37.4
|
1.0
|
C28
|
H:HVY601
|
4.0
|
47.5
|
1.0
|
C26
|
H:HVY601
|
4.0
|
44.8
|
1.0
|
C13
|
H:HVY601
|
4.2
|
38.5
|
1.0
|
C27
|
H:HVY601
|
4.5
|
43.8
|
1.0
|
C22
|
H:HVY601
|
4.5
|
36.2
|
1.0
|
CG
|
H:LEU393
|
4.7
|
30.9
|
1.0
|
CA
|
H:ALA403
|
4.7
|
35.9
|
1.0
|
OG1
|
H:THR338
|
4.7
|
40.2
|
1.0
|
C12
|
H:HVY601
|
4.8
|
39.2
|
1.0
|
N
|
H:ASP404
|
4.8
|
41.5
|
1.0
|
|
Reference:
D.Gurbani,
A.K.Bera,
K.Westover.
Dgy-06-116, A Novel and Selective Covalent Inhibitor of Src Kinase To Be Published.
Page generated: Sat Jul 27 22:08:18 2024
|