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Fluorine in PDB 5vam: Braf in Complex with RAF709

Enzymatic activity of Braf in Complex with RAF709

All present enzymatic activity of Braf in Complex with RAF709:
2.7.11.1;

Protein crystallography data

The structure of Braf in Complex with RAF709, PDB code: 5vam was solved by M.Mamo, B.A.Appleton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.75 / 2.10
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 109.390, 109.390, 135.980, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 22.3

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Braf in Complex with RAF709 (pdb code 5vam). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Braf in Complex with RAF709, PDB code: 5vam:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5vam

Go back to Fluorine Binding Sites List in 5vam
Fluorine binding site 1 out of 6 in the Braf in Complex with RAF709


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Braf in Complex with RAF709 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:35.8
occ:1.00
F33 A:92J801 0.0 35.8 1.0
C30 A:92J801 1.4 30.9 1.0
F31 A:92J801 2.2 30.2 1.0
F32 A:92J801 2.2 33.0 1.0
C27 A:92J801 2.4 28.2 1.0
C28 A:92J801 2.8 25.4 1.0
C A:GLY593 3.5 23.5 1.0
NE2 A:HIS574 3.5 25.1 1.0
O A:GLY593 3.6 20.3 1.0
CA A:GLY593 3.6 20.9 1.0
CD2 A:HIS574 3.6 25.5 1.0
C26 A:92J801 3.6 28.8 1.0
O A:ILE592 3.9 20.5 1.0
N A:GLY593 3.9 20.6 1.0
CG2 A:ILE592 3.9 23.5 1.0
C A:ILE592 4.0 21.7 1.0
N A:ASP594 4.1 23.8 1.0
C23 A:92J801 4.2 23.9 1.0
CD1 A:LEU567 4.4 20.8 1.0
CE1 A:HIS574 4.6 25.2 1.0
CB A:ILE592 4.7 22.1 1.0
CB A:ASP594 4.7 26.8 1.0
CG A:HIS574 4.7 24.8 1.0
C25 A:92J801 4.8 30.1 1.0
CG2 A:ILE513 4.8 15.9 1.0
CA A:ASP594 4.9 24.5 1.0
O29 A:92J801 4.9 24.4 1.0
C24 A:92J801 5.0 27.5 1.0
CA A:ILE592 5.0 18.7 1.0

Fluorine binding site 2 out of 6 in 5vam

Go back to Fluorine Binding Sites List in 5vam
Fluorine binding site 2 out of 6 in the Braf in Complex with RAF709


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Braf in Complex with RAF709 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:33.0
occ:1.00
F32 A:92J801 0.0 33.0 1.0
C30 A:92J801 1.3 30.9 1.0
F31 A:92J801 2.2 30.2 1.0
F33 A:92J801 2.2 35.8 1.0
C27 A:92J801 2.3 28.2 1.0
C28 A:92J801 3.1 25.4 1.0
C26 A:92J801 3.2 28.8 1.0
CG2 A:ILE513 3.6 15.9 1.0
CD2 A:LEU567 3.8 20.2 1.0
CD1 A:LEU567 4.3 20.8 1.0
C23 A:92J801 4.4 23.9 1.0
CD2 A:LEU505 4.4 26.3 1.0
C25 A:92J801 4.4 30.1 1.0
CG2 A:THR508 4.6 21.1 1.0
O A:ILE592 4.7 20.5 1.0
CG A:LEU567 4.7 21.9 1.0
CG1 A:VAL504 4.9 27.4 1.0
C24 A:92J801 4.9 27.5 1.0
CB A:ILE513 5.0 18.6 1.0
CD1 A:ILE513 5.0 19.1 1.0

Fluorine binding site 3 out of 6 in 5vam

Go back to Fluorine Binding Sites List in 5vam
Fluorine binding site 3 out of 6 in the Braf in Complex with RAF709


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Braf in Complex with RAF709 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:30.2
occ:1.00
F31 A:92J801 0.0 30.2 1.0
C30 A:92J801 1.4 30.9 1.0
F33 A:92J801 2.2 35.8 1.0
F32 A:92J801 2.2 33.0 1.0
C27 A:92J801 2.4 28.2 1.0
C26 A:92J801 2.9 28.8 1.0
CD2 A:HIS574 3.6 25.5 1.0
C28 A:92J801 3.7 25.4 1.0
CD1 A:LEU567 3.7 20.8 1.0
CH2 A:TRP604 3.8 55.1 1.0
NE2 A:HIS574 4.1 25.1 1.0
CD2 A:LEU567 4.2 20.2 1.0
CG A:HIS574 4.2 24.8 1.0
C25 A:92J801 4.2 30.1 1.0
CZ3 A:TRP604 4.3 54.9 1.0
CG2 A:ILE572 4.4 24.9 1.0
CZ2 A:TRP604 4.5 55.0 1.0
CG A:LEU567 4.6 21.9 1.0
CG1 A:VAL504 4.7 27.4 1.0
CB A:HIS574 4.8 22.3 1.0
C23 A:92J801 4.8 23.9 1.0
CA A:HIS574 4.8 22.5 1.0
CE1 A:HIS574 4.9 25.2 1.0

Fluorine binding site 4 out of 6 in 5vam

Go back to Fluorine Binding Sites List in 5vam
Fluorine binding site 4 out of 6 in the Braf in Complex with RAF709


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Braf in Complex with RAF709 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:32.2
occ:1.00
F33 B:92J801 0.0 32.2 1.0
C30 B:92J801 1.4 32.7 1.0
F31 B:92J801 2.2 35.2 1.0
F32 B:92J801 2.2 35.5 1.0
C27 B:92J801 2.4 28.9 1.0
C28 B:92J801 2.8 24.2 1.0
CA B:GLY593 3.4 21.2 1.0
C B:GLY593 3.5 23.5 1.0
C26 B:92J801 3.6 31.5 1.0
O B:GLY593 3.6 23.0 1.0
CD2 B:HIS574 3.7 25.0 1.0
NE2 B:HIS574 3.7 24.9 1.0
N B:GLY593 3.8 21.7 1.0
CG2 B:ILE592 4.0 16.9 1.0
O B:ILE592 4.0 22.1 1.0
C B:ILE592 4.1 23.1 1.0
N B:ASP594 4.1 21.1 1.0
C23 B:92J801 4.2 24.3 1.0
CD1 B:LEU567 4.4 22.9 1.0
C25 B:92J801 4.7 33.0 1.0
CG B:HIS574 4.8 24.4 1.0
CE1 B:HIS574 4.8 24.6 1.0
O29 B:92J801 4.9 21.6 1.0
CB B:ASP594 4.9 23.6 1.0
C24 B:92J801 4.9 30.2 1.0
CB B:ILE592 5.0 19.5 1.0
CG2 B:ILE513 5.0 19.4 1.0

Fluorine binding site 5 out of 6 in 5vam

Go back to Fluorine Binding Sites List in 5vam
Fluorine binding site 5 out of 6 in the Braf in Complex with RAF709


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Braf in Complex with RAF709 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:35.5
occ:1.00
F32 B:92J801 0.0 35.5 1.0
C30 B:92J801 1.3 32.7 1.0
F33 B:92J801 2.2 32.2 1.0
F31 B:92J801 2.2 35.2 1.0
C27 B:92J801 2.3 28.9 1.0
C28 B:92J801 3.1 24.2 1.0
C26 B:92J801 3.2 31.5 1.0
CG2 B:ILE513 3.7 19.4 1.0
CD2 B:LEU567 4.1 21.9 1.0
CD2 B:LEU505 4.2 27.9 1.0
C23 B:92J801 4.3 24.3 1.0
CD1 B:LEU567 4.5 22.9 1.0
C25 B:92J801 4.5 33.0 1.0
CG2 B:THR508 4.7 22.6 1.0
O B:ILE592 4.7 22.1 1.0
CG1 B:VAL504 4.8 25.9 1.0
CA B:GLY593 4.9 21.2 1.0
C24 B:92J801 4.9 30.2 1.0
CG B:LEU567 4.9 23.3 1.0
OG1 B:THR508 5.0 22.4 1.0

Fluorine binding site 6 out of 6 in 5vam

Go back to Fluorine Binding Sites List in 5vam
Fluorine binding site 6 out of 6 in the Braf in Complex with RAF709


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Braf in Complex with RAF709 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:35.2
occ:1.00
F31 B:92J801 0.0 35.2 1.0
C30 B:92J801 1.4 32.7 1.0
F33 B:92J801 2.2 32.2 1.0
F32 B:92J801 2.2 35.5 1.0
C27 B:92J801 2.4 28.9 1.0
C26 B:92J801 2.8 31.5 1.0
CH2 B:TRP604 3.5 43.1 0.8
C28 B:92J801 3.6 24.2 1.0
CD1 B:LEU567 3.9 22.9 1.0
CD2 B:HIS574 4.0 25.0 1.0
CZ3 B:TRP604 4.1 42.6 0.8
C25 B:92J801 4.2 33.0 1.0
CG2 B:ILE572 4.2 24.9 1.0
CZ2 B:TRP604 4.2 43.2 0.8
CD2 B:LEU567 4.3 21.9 1.0
NE2 B:HIS574 4.4 24.9 1.0
CG1 B:VAL504 4.5 25.9 1.0
CG B:HIS574 4.6 24.4 1.0
CG B:LEU567 4.7 23.3 1.0
C23 B:92J801 4.8 24.3 1.0
C24 B:92J801 5.0 30.2 1.0

Reference:

G.A.Nishiguchi, A.Rico, H.Tanner, R.J.Aversa, B.R.Taft, S.Subramanian, L.Setti, M.T.Burger, L.Wan, V.Tamez, A.Smith, Y.Lou, P.A.Barsanti, B.A.Appleton, M.Mamo, L.Tandeske, I.Dix, J.E.Tellew, S.Huang, L.A.Mathews Griner, V.G.Cooke, A.Van Abbema, H.Merritt, S.Ma, K.Gampa, F.Feng, J.Yuan, Y.Wang, J.R.Haling, S.Vaziri, M.Hekmat-Nejad, J.M.Jansen, V.Polyakov, R.Zang, V.Sethuraman, P.Amiri, M.Singh, E.Lees, W.Shao, D.D.Stuart, M.P.Dillon, S.Ramurthy. Design and Discovery of N-(2-Methyl-5'-Morpholino-6'-((Tetrahydro-2H-Pyran-4-Yl)Oxy) -[3,3'-Bipyridin]-5-Yl)-3-(Trifluoromethyl)Benzamide (RAF709): A Potent, Selective, and Efficacious Raf Inhibitor Targeting Ras Mutant Cancers. J. Med. Chem. V. 60 4869 2017.
ISSN: ISSN 1520-4804
PubMed: 28557458
DOI: 10.1021/ACS.JMEDCHEM.6B01862
Page generated: Thu Aug 1 16:02:53 2024

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