Fluorine in PDB 3oy3: Crystal Structure of Abl T315I Mutant Kinase Domain Bound with A Dfg- Out Inhibitor AP24589
Enzymatic activity of Crystal Structure of Abl T315I Mutant Kinase Domain Bound with A Dfg- Out Inhibitor AP24589
All present enzymatic activity of Crystal Structure of Abl T315I Mutant Kinase Domain Bound with A Dfg- Out Inhibitor AP24589:
2.7.10.2;
Protein crystallography data
The structure of Crystal Structure of Abl T315I Mutant Kinase Domain Bound with A Dfg- Out Inhibitor AP24589, PDB code: 3oy3
was solved by
T.Zhou,
L.Commodore,
W.S.Huang,
Y.Wang,
M.Thomas,
J.Keats,
Q.Xu,
V.Rivera,
W.C.Shakespeare,
T.Clackson,
D.C.Dalgarno,
X.Zhu,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
50.00 /
1.95
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
66.471,
59.988,
89.439,
90.00,
97.97,
90.00
|
R / Rfree (%)
|
22 /
26.6
|
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of Abl T315I Mutant Kinase Domain Bound with A Dfg- Out Inhibitor AP24589
(pdb code 3oy3). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the
Crystal Structure of Abl T315I Mutant Kinase Domain Bound with A Dfg- Out Inhibitor AP24589, PDB code: 3oy3:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 3oy3
Go back to
Fluorine Binding Sites List in 3oy3
Fluorine binding site 1 out
of 6 in the Crystal Structure of Abl T315I Mutant Kinase Domain Bound with A Dfg- Out Inhibitor AP24589
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Crystal Structure of Abl T315I Mutant Kinase Domain Bound with A Dfg- Out Inhibitor AP24589 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1
b:19.2
occ:1.00
|
F1
|
A:XY31
|
0.0
|
19.2
|
1.0
|
C19
|
A:XY31
|
1.3
|
17.1
|
1.0
|
F2
|
A:XY31
|
2.1
|
17.1
|
1.0
|
F3
|
A:XY31
|
2.2
|
18.1
|
1.0
|
C17
|
A:XY31
|
2.3
|
14.6
|
1.0
|
C16
|
A:XY31
|
3.1
|
15.6
|
1.0
|
C20
|
A:XY31
|
3.2
|
13.8
|
1.0
|
CD2
|
A:HIS361
|
3.3
|
13.3
|
1.0
|
C18
|
A:XY31
|
3.4
|
12.8
|
1.0
|
NE2
|
A:HIS361
|
3.4
|
13.0
|
1.0
|
O
|
A:ALA380
|
3.7
|
12.3
|
1.0
|
C
|
A:ALA380
|
3.8
|
11.2
|
1.0
|
CG1
|
A:VAL379
|
3.8
|
15.6
|
1.0
|
CB
|
A:ASP381
|
4.1
|
15.9
|
1.0
|
C21
|
A:XY31
|
4.2
|
14.6
|
1.0
|
CA
|
A:ALA380
|
4.2
|
10.0
|
1.0
|
N3
|
A:XY31
|
4.2
|
13.8
|
1.0
|
N
|
A:ASP381
|
4.3
|
11.3
|
1.0
|
CG
|
A:HIS361
|
4.3
|
12.7
|
1.0
|
CD2
|
A:LEU298
|
4.3
|
11.3
|
1.0
|
CE1
|
A:HIS361
|
4.4
|
11.9
|
1.0
|
C15
|
A:XY31
|
4.4
|
14.4
|
1.0
|
N
|
A:ALA380
|
4.5
|
11.9
|
1.0
|
CD1
|
A:LEU354
|
4.5
|
12.8
|
1.0
|
O
|
A:VAL379
|
4.6
|
9.9
|
1.0
|
C13
|
A:XY31
|
4.6
|
14.9
|
1.0
|
C
|
A:VAL379
|
4.6
|
10.2
|
1.0
|
CA
|
A:ASP381
|
4.8
|
15.1
|
1.0
|
ND1
|
A:HIS361
|
4.8
|
12.0
|
1.0
|
|
Fluorine binding site 2 out
of 6 in 3oy3
Go back to
Fluorine Binding Sites List in 3oy3
Fluorine binding site 2 out
of 6 in the Crystal Structure of Abl T315I Mutant Kinase Domain Bound with A Dfg- Out Inhibitor AP24589
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Crystal Structure of Abl T315I Mutant Kinase Domain Bound with A Dfg- Out Inhibitor AP24589 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1
b:17.1
occ:1.00
|
F2
|
A:XY31
|
0.0
|
17.1
|
1.0
|
C19
|
A:XY31
|
1.3
|
17.1
|
1.0
|
F1
|
A:XY31
|
2.1
|
19.2
|
1.0
|
F3
|
A:XY31
|
2.1
|
18.1
|
1.0
|
C17
|
A:XY31
|
2.4
|
14.6
|
1.0
|
C18
|
A:XY31
|
2.8
|
12.8
|
1.0
|
O
|
A:VAL379
|
3.1
|
9.9
|
1.0
|
CA
|
A:ALA380
|
3.4
|
10.0
|
1.0
|
C
|
A:VAL379
|
3.6
|
10.2
|
1.0
|
CG2
|
A:VAL299
|
3.7
|
11.0
|
1.0
|
CD2
|
A:LEU298
|
3.7
|
11.3
|
1.0
|
C16
|
A:XY31
|
3.7
|
15.6
|
1.0
|
C
|
A:ALA380
|
3.8
|
11.2
|
1.0
|
N
|
A:ALA380
|
3.8
|
11.9
|
1.0
|
CG1
|
A:VAL379
|
4.1
|
15.6
|
1.0
|
O
|
A:ALA380
|
4.2
|
12.3
|
1.0
|
C13
|
A:XY31
|
4.2
|
14.9
|
1.0
|
N
|
A:ASP381
|
4.3
|
11.3
|
1.0
|
N
|
A:VAL299
|
4.3
|
13.7
|
1.0
|
C20
|
A:XY31
|
4.4
|
13.8
|
1.0
|
O1
|
A:XY31
|
4.4
|
12.4
|
1.0
|
CB
|
A:LEU298
|
4.6
|
9.5
|
1.0
|
CB
|
A:ALA380
|
4.6
|
10.0
|
1.0
|
CB
|
A:VAL379
|
4.7
|
14.1
|
1.0
|
CB
|
A:VAL299
|
4.8
|
13.0
|
1.0
|
CA
|
A:VAL379
|
4.8
|
12.0
|
1.0
|
CG
|
A:LEU298
|
4.8
|
13.2
|
1.0
|
CA
|
A:LEU298
|
4.9
|
12.3
|
1.0
|
C15
|
A:XY31
|
4.9
|
14.4
|
1.0
|
CG1
|
A:VAL299
|
4.9
|
11.5
|
1.0
|
NE2
|
A:HIS361
|
5.0
|
13.0
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 3oy3
Go back to
Fluorine Binding Sites List in 3oy3
Fluorine binding site 3 out
of 6 in the Crystal Structure of Abl T315I Mutant Kinase Domain Bound with A Dfg- Out Inhibitor AP24589
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Crystal Structure of Abl T315I Mutant Kinase Domain Bound with A Dfg- Out Inhibitor AP24589 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1
b:18.1
occ:1.00
|
F3
|
A:XY31
|
0.0
|
18.1
|
1.0
|
C19
|
A:XY31
|
1.3
|
17.1
|
1.0
|
F2
|
A:XY31
|
2.1
|
17.1
|
1.0
|
F1
|
A:XY31
|
2.2
|
19.2
|
1.0
|
C17
|
A:XY31
|
2.4
|
14.6
|
1.0
|
C20
|
A:XY31
|
3.0
|
13.8
|
1.0
|
C16
|
A:XY31
|
3.0
|
15.6
|
1.0
|
CD1
|
A:ILE293
|
3.3
|
16.6
|
1.0
|
C18
|
A:XY31
|
3.5
|
12.8
|
1.0
|
CD2
|
A:LEU298
|
3.8
|
11.3
|
1.0
|
CD2
|
A:LEU354
|
4.3
|
14.8
|
1.0
|
C15
|
A:XY31
|
4.3
|
14.4
|
1.0
|
N3
|
A:XY31
|
4.3
|
13.8
|
1.0
|
CG2
|
A:ILE293
|
4.4
|
11.8
|
1.0
|
CG1
|
A:ILE293
|
4.5
|
15.2
|
1.0
|
CD1
|
A:LEU354
|
4.5
|
12.8
|
1.0
|
C13
|
A:XY31
|
4.7
|
14.9
|
1.0
|
CG
|
A:LEU298
|
4.8
|
13.2
|
1.0
|
CB
|
A:LEU298
|
4.8
|
9.5
|
1.0
|
CB
|
A:ILE293
|
4.9
|
16.5
|
1.0
|
CD1
|
A:LEU298
|
5.0
|
13.9
|
1.0
|
O
|
A:VAL379
|
5.0
|
9.9
|
1.0
|
CG
|
A:LEU354
|
5.0
|
14.4
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 3oy3
Go back to
Fluorine Binding Sites List in 3oy3
Fluorine binding site 4 out
of 6 in the Crystal Structure of Abl T315I Mutant Kinase Domain Bound with A Dfg- Out Inhibitor AP24589
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Crystal Structure of Abl T315I Mutant Kinase Domain Bound with A Dfg- Out Inhibitor AP24589 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F1
b:26.0
occ:1.00
|
F1
|
B:XY31
|
0.0
|
26.0
|
1.0
|
C19
|
B:XY31
|
1.3
|
27.4
|
1.0
|
F2
|
B:XY31
|
2.1
|
27.6
|
1.0
|
F3
|
B:XY31
|
2.2
|
27.5
|
1.0
|
C17
|
B:XY31
|
2.3
|
25.9
|
1.0
|
C16
|
B:XY31
|
3.2
|
25.2
|
1.0
|
CD2
|
B:HIS361
|
3.2
|
24.7
|
1.0
|
C18
|
B:XY31
|
3.3
|
25.4
|
1.0
|
NE2
|
B:HIS361
|
3.3
|
24.0
|
1.0
|
C20
|
B:XY31
|
3.4
|
24.7
|
1.0
|
O
|
B:ALA380
|
3.7
|
19.8
|
1.0
|
C
|
B:ALA380
|
3.8
|
18.0
|
1.0
|
CG1
|
B:VAL379
|
3.9
|
20.4
|
1.0
|
CB
|
B:ASP381
|
4.1
|
23.8
|
1.0
|
CA
|
B:ALA380
|
4.2
|
17.8
|
1.0
|
N
|
B:ASP381
|
4.2
|
20.2
|
1.0
|
CG
|
B:HIS361
|
4.2
|
25.3
|
1.0
|
CD2
|
B:LEU298
|
4.2
|
22.8
|
1.0
|
C21
|
B:XY31
|
4.3
|
25.2
|
1.0
|
N3
|
B:XY31
|
4.4
|
25.8
|
1.0
|
CE1
|
B:HIS361
|
4.4
|
21.6
|
1.0
|
N
|
B:ALA380
|
4.5
|
18.1
|
1.0
|
C15
|
B:XY31
|
4.5
|
25.8
|
1.0
|
O
|
B:VAL379
|
4.5
|
18.8
|
1.0
|
C
|
B:VAL379
|
4.6
|
19.0
|
1.0
|
CD1
|
B:LEU354
|
4.6
|
27.2
|
1.0
|
C13
|
B:XY31
|
4.6
|
25.3
|
1.0
|
CA
|
B:ASP381
|
4.8
|
23.7
|
1.0
|
ND1
|
B:HIS361
|
4.9
|
23.4
|
1.0
|
CB
|
B:VAL379
|
5.0
|
22.7
|
1.0
|
|
Fluorine binding site 5 out
of 6 in 3oy3
Go back to
Fluorine Binding Sites List in 3oy3
Fluorine binding site 5 out
of 6 in the Crystal Structure of Abl T315I Mutant Kinase Domain Bound with A Dfg- Out Inhibitor AP24589
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of Crystal Structure of Abl T315I Mutant Kinase Domain Bound with A Dfg- Out Inhibitor AP24589 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F1
b:27.6
occ:1.00
|
F2
|
B:XY31
|
0.0
|
27.6
|
1.0
|
C19
|
B:XY31
|
1.3
|
27.4
|
1.0
|
F3
|
B:XY31
|
2.1
|
27.5
|
1.0
|
F1
|
B:XY31
|
2.1
|
26.0
|
1.0
|
C17
|
B:XY31
|
2.4
|
25.9
|
1.0
|
C18
|
B:XY31
|
2.8
|
25.4
|
1.0
|
O
|
B:VAL379
|
3.0
|
18.8
|
1.0
|
CA
|
B:ALA380
|
3.5
|
17.8
|
1.0
|
CD2
|
B:LEU298
|
3.5
|
22.8
|
1.0
|
C
|
B:VAL379
|
3.6
|
19.0
|
1.0
|
CG2
|
B:VAL299
|
3.7
|
26.1
|
1.0
|
C16
|
B:XY31
|
3.8
|
25.2
|
1.0
|
C
|
B:ALA380
|
3.8
|
18.0
|
1.0
|
N
|
B:ALA380
|
3.9
|
18.1
|
1.0
|
C13
|
B:XY31
|
4.2
|
25.3
|
1.0
|
N
|
B:ASP381
|
4.3
|
20.2
|
1.0
|
O
|
B:ALA380
|
4.3
|
19.8
|
1.0
|
CG1
|
B:VAL379
|
4.3
|
20.4
|
1.0
|
N
|
B:VAL299
|
4.3
|
25.9
|
1.0
|
O1
|
B:XY31
|
4.3
|
20.4
|
1.0
|
C20
|
B:XY31
|
4.5
|
24.7
|
1.0
|
CB
|
B:LEU298
|
4.6
|
22.3
|
1.0
|
CG
|
B:LEU298
|
4.7
|
23.2
|
1.0
|
CB
|
B:ALA380
|
4.7
|
13.0
|
1.0
|
CB
|
B:VAL379
|
4.7
|
22.7
|
1.0
|
CA
|
B:VAL379
|
4.8
|
20.8
|
1.0
|
CB
|
B:VAL299
|
4.8
|
26.4
|
1.0
|
CA
|
B:LEU298
|
4.9
|
24.1
|
1.0
|
C15
|
B:XY31
|
4.9
|
25.8
|
1.0
|
CG1
|
B:VAL299
|
4.9
|
27.4
|
1.0
|
|
Fluorine binding site 6 out
of 6 in 3oy3
Go back to
Fluorine Binding Sites List in 3oy3
Fluorine binding site 6 out
of 6 in the Crystal Structure of Abl T315I Mutant Kinase Domain Bound with A Dfg- Out Inhibitor AP24589
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of Crystal Structure of Abl T315I Mutant Kinase Domain Bound with A Dfg- Out Inhibitor AP24589 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F1
b:27.5
occ:1.00
|
F3
|
B:XY31
|
0.0
|
27.5
|
1.0
|
C19
|
B:XY31
|
1.3
|
27.4
|
1.0
|
F2
|
B:XY31
|
2.1
|
27.6
|
1.0
|
F1
|
B:XY31
|
2.2
|
26.0
|
1.0
|
C17
|
B:XY31
|
2.4
|
25.9
|
1.0
|
C16
|
B:XY31
|
3.0
|
25.2
|
1.0
|
C20
|
B:XY31
|
3.0
|
24.7
|
1.0
|
CD1
|
B:ILE293
|
3.2
|
27.1
|
1.0
|
C18
|
B:XY31
|
3.5
|
25.4
|
1.0
|
CD2
|
B:LEU298
|
3.6
|
22.8
|
1.0
|
CD2
|
B:LEU354
|
4.2
|
25.6
|
1.0
|
CG2
|
B:ILE293
|
4.4
|
29.0
|
1.0
|
C15
|
B:XY31
|
4.4
|
25.8
|
1.0
|
N3
|
B:XY31
|
4.4
|
25.8
|
1.0
|
CG1
|
B:ILE293
|
4.5
|
29.8
|
1.0
|
CD1
|
B:LEU354
|
4.5
|
27.2
|
1.0
|
CG
|
B:LEU298
|
4.6
|
23.2
|
1.0
|
C13
|
B:XY31
|
4.8
|
25.3
|
1.0
|
CB
|
B:LEU298
|
4.9
|
22.3
|
1.0
|
CB
|
B:ILE293
|
4.9
|
31.6
|
1.0
|
CD1
|
B:LEU298
|
4.9
|
21.5
|
1.0
|
O
|
B:VAL379
|
4.9
|
18.8
|
1.0
|
CG
|
B:LEU354
|
4.9
|
27.1
|
1.0
|
C21
|
B:XY31
|
5.0
|
25.2
|
1.0
|
|
Reference:
T.Zhou,
L.Commodore,
W.S.Huang,
Y.Wang,
M.Thomas,
J.Keats,
Q.Xu,
V.M.Rivera,
W.C.Shakespeare,
T.Clackson,
D.C.Dalgarno,
X.Zhu.
Structural Mechanism of the Pan-Bcr-Abl Inhibitor Ponatinib (AP24534): Lessons For Overcoming Kinase Inhibitor Resistance. Chem.Biol.Drug Des. V. 77 1 2011.
ISSN: ISSN 1747-0277
PubMed: 21118377
DOI: 10.1111/J.1747-0285.2010.01054.X
Page generated: Wed Jul 31 21:28:57 2024
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