Fluorine in PDB 6p3d: The Co-Crystal Structure of Braf(V600E) with Ponatinib
Enzymatic activity of The Co-Crystal Structure of Braf(V600E) with Ponatinib
All present enzymatic activity of The Co-Crystal Structure of Braf(V600E) with Ponatinib:
2.7.11.1;
Protein crystallography data
The structure of The Co-Crystal Structure of Braf(V600E) with Ponatinib, PDB code: 6p3d
was solved by
B.Agianian,
E.Gavathiotis,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
84.03 /
2.11
|
Space group
|
P 43 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
118.839,
118.839,
51.530,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18.5 /
24.5
|
Fluorine Binding Sites:
The binding sites of Fluorine atom in the The Co-Crystal Structure of Braf(V600E) with Ponatinib
(pdb code 6p3d). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the
The Co-Crystal Structure of Braf(V600E) with Ponatinib, PDB code: 6p3d:
Jump to Fluorine binding site number:
1;
2;
3;
Fluorine binding site 1 out
of 3 in 6p3d
Go back to
Fluorine Binding Sites List in 6p3d
Fluorine binding site 1 out
of 3 in the The Co-Crystal Structure of Braf(V600E) with Ponatinib
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of The Co-Crystal Structure of Braf(V600E) with Ponatinib within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1001
b:23.7
occ:1.00
|
F1
|
A:0LI1001
|
0.0
|
23.7
|
1.0
|
C19
|
A:0LI1001
|
1.4
|
22.2
|
1.0
|
F3
|
A:0LI1001
|
2.2
|
23.8
|
1.0
|
F2
|
A:0LI1001
|
2.2
|
23.9
|
1.0
|
C17
|
A:0LI1001
|
2.4
|
20.8
|
1.0
|
C20
|
A:0LI1001
|
2.9
|
20.1
|
1.0
|
C16
|
A:0LI1001
|
2.9
|
19.6
|
1.0
|
C18
|
A:0LI1001
|
3.5
|
20.2
|
1.0
|
CG2
|
A:ILE513
|
4.0
|
15.1
|
1.0
|
CD2
|
A:LEU567
|
4.1
|
19.6
|
1.0
|
C15
|
A:0LI1001
|
4.3
|
19.3
|
1.0
|
N3
|
A:0LI1001
|
4.3
|
19.5
|
1.0
|
CG2
|
A:THR508
|
4.3
|
20.3
|
1.0
|
CD2
|
A:LEU505
|
4.4
|
21.7
|
1.0
|
CD1
|
A:LEU567
|
4.4
|
19.9
|
1.0
|
C13
|
A:0LI1001
|
4.7
|
18.5
|
1.0
|
C24
|
A:0LI1001
|
4.9
|
18.8
|
1.0
|
CG
|
A:LEU567
|
4.9
|
19.6
|
1.0
|
C21
|
A:0LI1001
|
5.0
|
18.9
|
1.0
|
C14
|
A:0LI1001
|
5.0
|
19.7
|
1.0
|
CD1
|
A:ILE513
|
5.0
|
19.1
|
1.0
|
|
Fluorine binding site 2 out
of 3 in 6p3d
Go back to
Fluorine Binding Sites List in 6p3d
Fluorine binding site 2 out
of 3 in the The Co-Crystal Structure of Braf(V600E) with Ponatinib
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of The Co-Crystal Structure of Braf(V600E) with Ponatinib within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1001
b:23.9
occ:1.00
|
F2
|
A:0LI1001
|
0.0
|
23.9
|
1.0
|
C19
|
A:0LI1001
|
1.3
|
22.2
|
1.0
|
F3
|
A:0LI1001
|
2.1
|
23.8
|
1.0
|
F1
|
A:0LI1001
|
2.2
|
23.7
|
1.0
|
C17
|
A:0LI1001
|
2.3
|
20.8
|
1.0
|
C16
|
A:0LI1001
|
3.1
|
19.6
|
1.0
|
C20
|
A:0LI1001
|
3.2
|
20.1
|
1.0
|
C18
|
A:0LI1001
|
3.3
|
20.2
|
1.0
|
NE2
|
A:HIS574
|
3.3
|
21.8
|
1.0
|
CD2
|
A:HIS574
|
3.4
|
18.6
|
1.0
|
C
|
A:GLY593
|
3.7
|
20.6
|
1.0
|
CA
|
A:GLY593
|
3.8
|
18.2
|
1.0
|
O
|
A:GLY593
|
3.9
|
21.8
|
1.0
|
N
|
A:ASP594
|
4.0
|
20.6
|
1.0
|
C21
|
A:0LI1001
|
4.3
|
18.9
|
1.0
|
N3
|
A:0LI1001
|
4.3
|
19.5
|
1.0
|
O
|
A:ILE592
|
4.3
|
16.7
|
1.0
|
C15
|
A:0LI1001
|
4.3
|
19.3
|
1.0
|
CG2
|
A:ILE592
|
4.3
|
18.0
|
1.0
|
CE1
|
A:HIS574
|
4.3
|
19.0
|
1.0
|
CB
|
A:ASP594
|
4.4
|
19.4
|
1.0
|
N
|
A:GLY593
|
4.4
|
17.4
|
1.0
|
CG
|
A:HIS574
|
4.4
|
18.8
|
1.0
|
CD1
|
A:LEU567
|
4.5
|
19.9
|
1.0
|
C
|
A:ILE592
|
4.5
|
17.1
|
1.0
|
C13
|
A:0LI1001
|
4.5
|
18.5
|
1.0
|
CA
|
A:ASP594
|
4.8
|
20.3
|
1.0
|
C14
|
A:0LI1001
|
4.9
|
19.7
|
1.0
|
ND1
|
A:HIS574
|
4.9
|
18.2
|
1.0
|
|
Fluorine binding site 3 out
of 3 in 6p3d
Go back to
Fluorine Binding Sites List in 6p3d
Fluorine binding site 3 out
of 3 in the The Co-Crystal Structure of Braf(V600E) with Ponatinib
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of The Co-Crystal Structure of Braf(V600E) with Ponatinib within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1001
b:23.8
occ:1.00
|
F3
|
A:0LI1001
|
0.0
|
23.8
|
1.0
|
C19
|
A:0LI1001
|
1.3
|
22.2
|
1.0
|
F2
|
A:0LI1001
|
2.1
|
23.9
|
1.0
|
F1
|
A:0LI1001
|
2.2
|
23.7
|
1.0
|
C17
|
A:0LI1001
|
2.4
|
20.8
|
1.0
|
C18
|
A:0LI1001
|
2.8
|
20.2
|
1.0
|
O
|
A:ILE592
|
3.2
|
16.7
|
1.0
|
CA
|
A:GLY593
|
3.4
|
18.2
|
1.0
|
CG2
|
A:ILE513
|
3.5
|
15.1
|
1.0
|
C16
|
A:0LI1001
|
3.7
|
19.6
|
1.0
|
C
|
A:ILE592
|
3.9
|
17.1
|
1.0
|
C
|
A:GLY593
|
4.0
|
20.6
|
1.0
|
N
|
A:GLY593
|
4.1
|
17.4
|
1.0
|
C13
|
A:0LI1001
|
4.2
|
18.5
|
1.0
|
CD2
|
A:LEU505
|
4.2
|
21.7
|
1.0
|
N
|
A:ASP594
|
4.3
|
20.6
|
1.0
|
C20
|
A:0LI1001
|
4.3
|
20.1
|
1.0
|
O1
|
A:0LI1001
|
4.4
|
19.9
|
1.0
|
N
|
A:LEU514
|
4.7
|
18.2
|
1.0
|
CB
|
A:LEU514
|
4.8
|
18.0
|
1.0
|
O
|
A:GLY593
|
4.8
|
21.8
|
1.0
|
C15
|
A:0LI1001
|
4.8
|
19.3
|
1.0
|
CB
|
A:ILE513
|
4.8
|
16.5
|
1.0
|
CG2
|
A:ILE592
|
5.0
|
18.0
|
1.0
|
O
|
A:LEU514
|
5.0
|
18.4
|
1.0
|
C14
|
A:0LI1001
|
5.0
|
19.7
|
1.0
|
CD1
|
A:ILE513
|
5.0
|
19.1
|
1.0
|
|
Reference:
X.M.Cotto-Rios,
B.Agianian,
N.Gitego,
E.Zacharioudakis,
O.Giricz,
Y.Wu,
Y.Zou,
A.Verma,
P.I.Poulikakos,
E.Gavathiotis.
Inhibitors of Braf Dimers Using An Allosteric Site. Nat Commun V. 11 4370 2020.
ISSN: ESSN 2041-1723
PubMed: 32873792
DOI: 10.1038/S41467-020-18123-2
Page generated: Sun Dec 13 13:05:00 2020
|