Fluorine in PDB 4oys: Crystal Structure of VPS34 in Complex with SAR405.

All present enzymatic activity of Crystal Structure of VPS34 in Complex with SAR405.:
2.7.1.137;

The structure of Crystal Structure of VPS34 in Complex with SAR405., PDB code: 4oys was solved by M.Mathieu, J.P.Marquette, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	72.85 / 2.90
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	89.810, 145.700, 61.780, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 24.8

The structure of Crystal Structure of VPS34 in Complex with SAR405. also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Fluorine atom in the Crystal Structure of VPS34 in Complex with SAR405. (pdb code 4oys). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of VPS34 in Complex with SAR405., PDB code: 4oys:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of VPS34 in Complex with SAR405.


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 VPS34 in Complex with SAR405. within 5.0Å range: probe atom residue distance (Å) B Occ A:F905 b:47.4 occ:1.00 F14 A:1TT905 0.0 47.4 1.0 C13 A:1TT905 1.3 47.0 1.0 F15 A:1TT905 2.1 49.3 1.0 F16 A:1TT905 2.1 45.5 1.0 C8 A:1TT905 2.4 45.7 1.0 N7 A:1TT905 2.8 45.8 1.0 C6 A:1TT905 2.9 42.5 1.0 N5 A:1TT905 3.0 40.5 1.0 C10 A:1TT905 3.0 39.8 1.0 C9 A:1TT905 3.2 43.8 1.0 C22 A:1TT905 3.6 47.0 1.0 N4 A:1TT905 3.8 38.6 1.0 CD1 A:ILE634 3.8 57.1 1.0 CG2 A:ILE634 3.8 47.5 1.0 CE A:LYS636 3.9 53.1 1.0 C1 A:1TT905 4.0 41.0 1.0 CG A:PRO618 4.2 60.4 1.0 CB A:PRO618 4.5 55.7 1.0 O12 A:1TT905 4.6 43.8 1.0 C3 A:1TT905 4.6 36.0 1.0 NZ A:LYS636 4.7 57.7 1.0 C2 A:1TT905 4.7 37.2 1.0 CB A:ILE634 4.8 47.5 1.0 CG1 A:ILE634 4.8 48.2 1.0 CD A:LYS636 4.8 41.6 1.0 CG A:LYS636 5.0 38.5 1.0 C23 A:1TT905 5.0 52.3 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of VPS34 in Complex with SAR405.


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 VPS34 in Complex with SAR405. within 5.0Å range: probe atom residue distance (Å) B Occ A:F905 b:49.3 occ:1.00 F15 A:1TT905 0.0 49.3 1.0 C13 A:1TT905 1.3 47.0 1.0 F14 A:1TT905 2.1 47.4 1.0 F16 A:1TT905 2.1 45.5 1.0 C8 A:1TT905 2.3 45.7 1.0 N7 A:1TT905 3.0 45.8 1.0 C22 A:1TT905 3.2 47.0 1.0 CG A:PRO618 3.4 60.4 1.0 CG A:PHE612 3.4 58.2 1.0 CB A:PHE612 3.5 56.5 1.0 CD1 A:PHE612 3.6 61.0 1.0 C9 A:1TT905 3.7 43.8 1.0 CD2 A:PHE612 3.8 60.4 1.0 C6 A:1TT905 4.0 42.5 1.0 CB A:PRO618 4.2 55.7 1.0 CE1 A:PHE612 4.3 61.8 1.0 CB A:SER614 4.3 70.4 1.0 O A:HOH1004 4.3 31.7 1.0 C10 A:1TT905 4.4 39.8 1.0 CE2 A:PHE612 4.4 63.1 1.0 CD A:PRO618 4.5 56.1 1.0 N5 A:1TT905 4.5 40.5 1.0 CZ A:PHE612 4.6 61.1 1.0 C23 A:1TT905 4.6 52.3 1.0 CG2 A:ILE634 4.7 47.5 1.0 CD1 A:ILE634 4.7 57.1 1.0 N4 A:1TT905 4.8 38.6 1.0 OG A:SER614 4.9 75.1 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of VPS34 in Complex with SAR405.


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 VPS34 in Complex with SAR405. within 5.0Å range: probe atom residue distance (Å) B Occ A:F905 b:45.5 occ:1.00 F16 A:1TT905 0.0 45.5 1.0 C13 A:1TT905 1.3 47.0 1.0 F15 A:1TT905 2.1 49.3 1.0 F14 A:1TT905 2.1 47.4 1.0 C8 A:1TT905 2.4 45.7 1.0 C9 A:1TT905 2.8 43.8 1.0 C10 A:1TT905 3.3 39.8 1.0 CG A:PRO618 3.5 60.4 1.0 N7 A:1TT905 3.6 45.8 1.0 CB A:SER614 3.9 70.4 1.0 OG A:SER614 4.0 75.1 1.0 N5 A:1TT905 4.1 40.5 1.0 CE A:LYS636 4.3 53.1 1.0 C6 A:1TT905 4.3 42.5 1.0 CB A:PRO618 4.4 55.7 1.0 C22 A:1TT905 4.6 47.0 1.0 CD A:PRO618 4.7 56.1 1.0 NZ A:LYS636 4.7 57.7 1.0 CD A:LYS636 4.9 41.6 1.0

B.Ronan, O.Flamand, L.Vescovi, C.Dureuil, L.Durand, F.Fassy, M.-F.Bachelot, A.Lamberton, M.Mathieu, T.Bertrand, J.-P.Marquette, Y.El-Ahmad, B.Filoche-Romme, L.Schio, C.Garcia-Echeverria, H.Goulaouic, B.Pasquier. Highly Potent and Selective Kinase Inhibitor of VPS34 Affects Vesicle Trafficking and Autophagy, and Synergizes with Mtor Inhibitor in Tumor Cells Nat.Chem.Biol. 2014.
ISSN: ISSN 1552-4450
DOI: 10.1038/NCHEMBIO.1681