Fluorine in PDB 4e4x: Crystal Structure of B-Raf Kinase Domain in Complex with A Dihydropyrido[2,3-D]Pyrimidinone-Based Inhibitor
Enzymatic activity of Crystal Structure of B-Raf Kinase Domain in Complex with A Dihydropyrido[2,3-D]Pyrimidinone-Based Inhibitor
All present enzymatic activity of Crystal Structure of B-Raf Kinase Domain in Complex with A Dihydropyrido[2,3-D]Pyrimidinone-Based Inhibitor:
2.7.11.1;
Protein crystallography data
The structure of Crystal Structure of B-Raf Kinase Domain in Complex with A Dihydropyrido[2,3-D]Pyrimidinone-Based Inhibitor, PDB code: 4e4x
was solved by
W.C.Voegtli,
H.L.Sturgis,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.86 /
3.60
|
Space group
|
P 41 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
109.000,
109.000,
155.210,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
29.9 /
33.8
|
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of B-Raf Kinase Domain in Complex with A Dihydropyrido[2,3-D]Pyrimidinone-Based Inhibitor
(pdb code 4e4x). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the
Crystal Structure of B-Raf Kinase Domain in Complex with A Dihydropyrido[2,3-D]Pyrimidinone-Based Inhibitor, PDB code: 4e4x:
Jump to Fluorine binding site number:
1;
2;
3;
4;
Fluorine binding site 1 out
of 4 in 4e4x
Go back to
Fluorine Binding Sites List in 4e4x
Fluorine binding site 1 out
of 4 in the Crystal Structure of B-Raf Kinase Domain in Complex with A Dihydropyrido[2,3-D]Pyrimidinone-Based Inhibitor
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 B-Raf Kinase Domain in Complex with A Dihydropyrido[2,3-D]Pyrimidinone-Based Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F801
b:53.7
occ:1.00
|
F19
|
A:T1Q801
|
0.0
|
53.7
|
1.0
|
C18
|
A:T1Q801
|
1.4
|
50.6
|
1.0
|
C13
|
A:T1Q801
|
2.4
|
51.0
|
1.0
|
C17
|
A:T1Q801
|
2.4
|
49.4
|
1.0
|
C9
|
A:T1Q801
|
2.8
|
51.4
|
1.0
|
C10
|
A:T1Q801
|
3.3
|
51.1
|
1.0
|
CB
|
A:ALA481
|
3.4
|
45.3
|
1.0
|
OG1
|
A:THR529
|
3.6
|
36.7
|
1.0
|
C14
|
A:T1Q801
|
3.7
|
50.5
|
1.0
|
C16
|
A:T1Q801
|
3.7
|
48.8
|
1.0
|
C8
|
A:T1Q801
|
3.7
|
52.0
|
1.0
|
C
|
A:ALA481
|
3.7
|
46.4
|
1.0
|
N
|
A:LYS483
|
3.7
|
56.6
|
1.0
|
O
|
A:ALA481
|
3.7
|
44.7
|
1.0
|
CB
|
A:LYS483
|
3.8
|
62.1
|
1.0
|
N
|
A:VAL482
|
3.9
|
49.0
|
1.0
|
C
|
A:VAL482
|
4.0
|
53.5
|
1.0
|
CG1
|
A:VAL471
|
4.0
|
56.0
|
1.0
|
O12
|
A:T1Q801
|
4.0
|
51.9
|
1.0
|
C15
|
A:T1Q801
|
4.2
|
49.5
|
1.0
|
CA
|
A:ALA481
|
4.2
|
45.3
|
1.0
|
CA
|
A:VAL482
|
4.3
|
51.6
|
1.0
|
CA
|
A:LYS483
|
4.3
|
61.1
|
1.0
|
CG2
|
A:THR529
|
4.3
|
38.5
|
1.0
|
C5
|
A:T1Q801
|
4.4
|
52.2
|
1.0
|
O
|
A:VAL482
|
4.5
|
53.2
|
1.0
|
O
|
A:ILE527
|
4.5
|
45.1
|
1.0
|
CB
|
A:THR529
|
4.5
|
37.6
|
1.0
|
N7
|
A:T1Q801
|
4.6
|
52.4
|
1.0
|
N
|
A:THR529
|
4.6
|
38.6
|
1.0
|
F20
|
A:T1Q801
|
4.8
|
53.3
|
1.0
|
CD
|
A:LYS483
|
4.8
|
65.3
|
1.0
|
CG2
|
A:VAL471
|
4.9
|
57.3
|
1.0
|
CG
|
A:LYS483
|
4.9
|
64.3
|
1.0
|
C4
|
A:T1Q801
|
5.0
|
52.9
|
1.0
|
|
Fluorine binding site 2 out
of 4 in 4e4x
Go back to
Fluorine Binding Sites List in 4e4x
Fluorine binding site 2 out
of 4 in the Crystal Structure of B-Raf Kinase Domain in Complex with A Dihydropyrido[2,3-D]Pyrimidinone-Based Inhibitor
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 B-Raf Kinase Domain in Complex with A Dihydropyrido[2,3-D]Pyrimidinone-Based Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F801
b:53.3
occ:1.00
|
F20
|
A:T1Q801
|
0.0
|
53.3
|
1.0
|
C14
|
A:T1Q801
|
1.4
|
50.5
|
1.0
|
C13
|
A:T1Q801
|
2.4
|
51.0
|
1.0
|
C15
|
A:T1Q801
|
2.4
|
49.5
|
1.0
|
N21
|
A:T1Q801
|
2.8
|
49.8
|
1.0
|
C9
|
A:T1Q801
|
2.8
|
51.4
|
1.0
|
C8
|
A:T1Q801
|
3.3
|
52.0
|
1.0
|
O12
|
A:T1Q801
|
3.3
|
51.9
|
1.0
|
CD2
|
A:LEU514
|
3.3
|
35.1
|
1.0
|
N
|
A:ASP594
|
3.4
|
45.7
|
1.0
|
C10
|
A:T1Q801
|
3.7
|
51.1
|
1.0
|
C18
|
A:T1Q801
|
3.7
|
50.6
|
1.0
|
C16
|
A:T1Q801
|
3.7
|
48.8
|
1.0
|
CA
|
A:GLY593
|
3.9
|
41.5
|
1.0
|
CE1
|
A:PHE583
|
3.9
|
34.4
|
1.0
|
C
|
A:GLY593
|
4.0
|
44.8
|
1.0
|
CA
|
A:ASP594
|
4.1
|
46.8
|
1.0
|
C17
|
A:T1Q801
|
4.2
|
49.4
|
1.0
|
CZ
|
A:PHE583
|
4.2
|
34.0
|
1.0
|
CB
|
A:ASP594
|
4.3
|
47.5
|
1.0
|
N7
|
A:T1Q801
|
4.3
|
52.4
|
1.0
|
S23
|
A:T1Q801
|
4.4
|
50.2
|
1.0
|
C5
|
A:T1Q801
|
4.7
|
52.2
|
1.0
|
F19
|
A:T1Q801
|
4.8
|
53.7
|
1.0
|
CG
|
A:LEU514
|
4.8
|
34.7
|
1.0
|
O
|
A:GLY593
|
4.9
|
47.3
|
1.0
|
C4
|
A:T1Q801
|
5.0
|
52.9
|
1.0
|
|
Fluorine binding site 3 out
of 4 in 4e4x
Go back to
Fluorine Binding Sites List in 4e4x
Fluorine binding site 3 out
of 4 in the Crystal Structure of B-Raf Kinase Domain in Complex with A Dihydropyrido[2,3-D]Pyrimidinone-Based Inhibitor
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 B-Raf Kinase Domain in Complex with A Dihydropyrido[2,3-D]Pyrimidinone-Based Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F801
b:48.9
occ:1.00
|
F19
|
B:T1Q801
|
0.0
|
48.9
|
1.0
|
C18
|
B:T1Q801
|
1.4
|
46.5
|
1.0
|
C13
|
B:T1Q801
|
2.4
|
46.4
|
1.0
|
C17
|
B:T1Q801
|
2.4
|
46.0
|
1.0
|
C9
|
B:T1Q801
|
2.8
|
45.8
|
1.0
|
CB
|
B:ALA481
|
3.3
|
45.0
|
1.0
|
C10
|
B:T1Q801
|
3.4
|
46.5
|
1.0
|
C8
|
B:T1Q801
|
3.5
|
45.2
|
1.0
|
C
|
B:ALA481
|
3.7
|
45.9
|
1.0
|
C14
|
B:T1Q801
|
3.7
|
45.8
|
1.0
|
C16
|
B:T1Q801
|
3.7
|
45.6
|
1.0
|
CG1
|
B:VAL471
|
3.7
|
54.1
|
1.0
|
OG1
|
B:THR529
|
3.7
|
36.9
|
1.0
|
N
|
B:LYS483
|
3.7
|
56.8
|
1.0
|
O
|
B:ALA481
|
3.8
|
45.7
|
1.0
|
CB
|
B:LYS483
|
3.8
|
61.5
|
1.0
|
O12
|
B:T1Q801
|
3.8
|
43.2
|
1.0
|
N
|
B:VAL482
|
3.9
|
47.1
|
1.0
|
C
|
B:VAL482
|
3.9
|
53.2
|
1.0
|
CA
|
B:ALA481
|
4.1
|
45.0
|
1.0
|
C15
|
B:T1Q801
|
4.2
|
44.9
|
1.0
|
CA
|
B:VAL482
|
4.2
|
50.2
|
1.0
|
CA
|
B:LYS483
|
4.2
|
60.5
|
1.0
|
O
|
B:VAL482
|
4.3
|
53.8
|
1.0
|
C5
|
B:T1Q801
|
4.5
|
46.2
|
1.0
|
N7
|
B:T1Q801
|
4.5
|
46.5
|
1.0
|
CG2
|
B:THR529
|
4.6
|
38.1
|
1.0
|
O
|
B:ILE527
|
4.6
|
43.6
|
1.0
|
CG2
|
B:VAL471
|
4.7
|
54.8
|
1.0
|
CB
|
B:THR529
|
4.7
|
37.1
|
1.0
|
CB
|
B:VAL471
|
4.8
|
54.7
|
1.0
|
F20
|
B:T1Q801
|
4.8
|
47.8
|
1.0
|
CD
|
B:LYS483
|
4.8
|
66.1
|
1.0
|
N
|
B:THR529
|
4.8
|
36.5
|
1.0
|
CG
|
B:LYS483
|
4.9
|
64.5
|
1.0
|
C4
|
B:T1Q801
|
5.0
|
46.5
|
1.0
|
|
Fluorine binding site 4 out
of 4 in 4e4x
Go back to
Fluorine Binding Sites List in 4e4x
Fluorine binding site 4 out
of 4 in the Crystal Structure of B-Raf Kinase Domain in Complex with A Dihydropyrido[2,3-D]Pyrimidinone-Based Inhibitor
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 B-Raf Kinase Domain in Complex with A Dihydropyrido[2,3-D]Pyrimidinone-Based Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F801
b:47.8
occ:1.00
|
F20
|
B:T1Q801
|
0.0
|
47.8
|
1.0
|
C14
|
B:T1Q801
|
1.4
|
45.8
|
1.0
|
C13
|
B:T1Q801
|
2.4
|
46.4
|
1.0
|
C15
|
B:T1Q801
|
2.4
|
44.9
|
1.0
|
N21
|
B:T1Q801
|
2.8
|
42.8
|
1.0
|
C9
|
B:T1Q801
|
2.8
|
45.8
|
1.0
|
CD2
|
B:LEU514
|
3.1
|
34.5
|
1.0
|
C8
|
B:T1Q801
|
3.4
|
45.2
|
1.0
|
O12
|
B:T1Q801
|
3.5
|
43.2
|
1.0
|
C10
|
B:T1Q801
|
3.5
|
46.5
|
1.0
|
CE1
|
B:PHE583
|
3.7
|
31.5
|
1.0
|
C18
|
B:T1Q801
|
3.7
|
46.5
|
1.0
|
C16
|
B:T1Q801
|
3.7
|
45.6
|
1.0
|
N
|
B:ASP594
|
3.7
|
44.0
|
1.0
|
CA
|
B:GLY593
|
4.0
|
39.5
|
1.0
|
CZ
|
B:PHE583
|
4.0
|
30.3
|
1.0
|
C
|
B:GLY593
|
4.1
|
41.9
|
1.0
|
C17
|
B:T1Q801
|
4.2
|
46.0
|
1.0
|
CA
|
B:ASP594
|
4.4
|
46.6
|
1.0
|
N7
|
B:T1Q801
|
4.4
|
46.5
|
1.0
|
S23
|
B:T1Q801
|
4.4
|
40.4
|
1.0
|
C27
|
B:T1Q801
|
4.5
|
34.1
|
1.0
|
CB
|
B:ASP594
|
4.5
|
47.1
|
1.0
|
CG
|
B:LEU514
|
4.6
|
35.8
|
1.0
|
C5
|
B:T1Q801
|
4.6
|
46.2
|
1.0
|
F19
|
B:T1Q801
|
4.8
|
48.9
|
1.0
|
CD1
|
B:PHE583
|
4.9
|
32.8
|
1.0
|
C4
|
B:T1Q801
|
4.9
|
46.5
|
1.0
|
|
Reference:
L.Ren,
K.A.Ahrendt,
J.Grina,
E.R.Laird,
A.J.Buckmelter,
J.D.Hansen,
B.Newhouse,
D.Moreno,
S.Wenglowsky,
V.Dinkel,
S.L.Gloor,
G.Hastings,
S.Rana,
K.Rasor,
T.Risom,
H.L.Sturgis,
W.C.Voegtli,
S.Mathieu.
The Discovery of Potent and Selective Pyridopyrimidin-7-One Based Inhibitors of B-Raf(V600E) Kinase. Bioorg.Med.Chem.Lett. V. 22 3387 2012.
ISSN: ISSN 0960-894X
PubMed: 22534450
DOI: 10.1016/J.BMCL.2012.04.015
Page generated: Thu Aug 1 01:16:34 2024
|