Fluorine in PDB 6p3d: 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;

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

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 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 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 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

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