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Fluorine in PDB 4uwg: Discovery of (2S)-8-((3R)-3-Methylmorpholin-4-Yl)-1-(3- Methyl-2-Oxo-Butyl)-2-(Trifluoromethyl)-3,4-Dihydro-2H- Pyrimido(1,2-A)Pyrimidin-6-One: A Novel Potent and Selective Inhibitor of VPS34 For the Treatment of Solid Tumors

Enzymatic activity of Discovery of (2S)-8-((3R)-3-Methylmorpholin-4-Yl)-1-(3- Methyl-2-Oxo-Butyl)-2-(Trifluoromethyl)-3,4-Dihydro-2H- Pyrimido(1,2-A)Pyrimidin-6-One: A Novel Potent and Selective Inhibitor of VPS34 For the Treatment of Solid Tumors

All present enzymatic activity of Discovery of (2S)-8-((3R)-3-Methylmorpholin-4-Yl)-1-(3- Methyl-2-Oxo-Butyl)-2-(Trifluoromethyl)-3,4-Dihydro-2H- Pyrimido(1,2-A)Pyrimidin-6-One: A Novel Potent and Selective Inhibitor of VPS34 For the Treatment of Solid Tumors:
2.7.1.137;

Protein crystallography data

The structure of Discovery of (2S)-8-((3R)-3-Methylmorpholin-4-Yl)-1-(3- Methyl-2-Oxo-Butyl)-2-(Trifluoromethyl)-3,4-Dihydro-2H- Pyrimido(1,2-A)Pyrimidin-6-One: A Novel Potent and Selective Inhibitor of VPS34 For the Treatment of Solid Tumors, PDB code: 4uwg was solved by B.Pasquier, Y.El-Ahmad, B.Filoche-Romme, C.Dureuil, F.Fassy, P.Y.Abecassis, M.Mathieu, T.Bertrand, T.Benard, C.Barriere, S.Elbatti, J.P.Letallec, V.Sonnefraud, M.Brollo, L.Delbarre, V.Loyau, F.Pilorge, L.Bertin, P.Richepin, J.Arigon, J.R.Labrosse, J.Clement, F.Durand, R.Combet, P.Perraut, V.Leroy, F.Gay, D.Lefrancois, F.Bretin, J.P.Marquette, N.Michot, A.Caron, C.Castell, L.Schio, G.Mccort, H.Goulaouic, C.Garcia-Echeverria, B.Ronan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.88 / 2.70
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 93.800, 147.010, 61.780, 90.00, 90.00, 90.00
R / Rfree (%) 18.03 / 22.11

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Discovery of (2S)-8-((3R)-3-Methylmorpholin-4-Yl)-1-(3- Methyl-2-Oxo-Butyl)-2-(Trifluoromethyl)-3,4-Dihydro-2H- Pyrimido(1,2-A)Pyrimidin-6-One: A Novel Potent and Selective Inhibitor of VPS34 For the Treatment of Solid Tumors (pdb code 4uwg). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Discovery of (2S)-8-((3R)-3-Methylmorpholin-4-Yl)-1-(3- Methyl-2-Oxo-Butyl)-2-(Trifluoromethyl)-3,4-Dihydro-2H- Pyrimido(1,2-A)Pyrimidin-6-One: A Novel Potent and Selective Inhibitor of VPS34 For the Treatment of Solid Tumors, PDB code: 4uwg:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 4uwg

Go back to Fluorine Binding Sites List in 4uwg
Fluorine binding site 1 out of 3 in the Discovery of (2S)-8-((3R)-3-Methylmorpholin-4-Yl)-1-(3- Methyl-2-Oxo-Butyl)-2-(Trifluoromethyl)-3,4-Dihydro-2H- Pyrimido(1,2-A)Pyrimidin-6-One: A Novel Potent and Selective Inhibitor of VPS34 For the Treatment of Solid Tumors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Discovery of (2S)-8-((3R)-3-Methylmorpholin-4-Yl)-1-(3- Methyl-2-Oxo-Butyl)-2-(Trifluoromethyl)-3,4-Dihydro-2H- Pyrimido(1,2-A)Pyrimidin-6-One: A Novel Potent and Selective Inhibitor of VPS34 For the Treatment of Solid Tumors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1873

b:54.9
occ:1.00
 F14 A:RBQ1873 0.0 54.9 1.0
C9 A:RBQ1873 1.3 53.3 1.0
F16 A:RBQ1873 2.1 54.2 1.0
F15 A:RBQ1873 2.1 54.9 1.0
C8 A:RBQ1873 2.4 49.6 1.0
C12 A:RBQ1873 2.9 48.1 1.0
CG A:PRO618 3.3 55.6 1.0
C11 A:RBQ1873 3.6 47.6 1.0
CB A:SER614 3.6 65.6 1.0
N5 A:RBQ1873 3.7 48.9 1.0
OG A:SER614 3.7 73.5 1.0
CD A:PRO618 4.2 51.5 1.0
N3 A:RBQ1873 4.4 48.0 1.0
CB A:PRO618 4.4 51.1 1.0
C1 A:RBQ1873 4.5 50.3 1.0
C18 A:RBQ1873 4.7 48.4 1.0
CB A:PHE612 4.8 53.4 1.0
CG A:PHE612 5.0 54.0 1.0

Fluorine binding site 2 out of 3 in 4uwg

Go back to Fluorine Binding Sites List in 4uwg
Fluorine binding site 2 out of 3 in the Discovery of (2S)-8-((3R)-3-Methylmorpholin-4-Yl)-1-(3- Methyl-2-Oxo-Butyl)-2-(Trifluoromethyl)-3,4-Dihydro-2H- Pyrimido(1,2-A)Pyrimidin-6-One: A Novel Potent and Selective Inhibitor of VPS34 For the Treatment of Solid Tumors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Discovery of (2S)-8-((3R)-3-Methylmorpholin-4-Yl)-1-(3- Methyl-2-Oxo-Butyl)-2-(Trifluoromethyl)-3,4-Dihydro-2H- Pyrimido(1,2-A)Pyrimidin-6-One: A Novel Potent and Selective Inhibitor of VPS34 For the Treatment of Solid Tumors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1873

b:54.9
occ:1.00
 F15 A:RBQ1873 0.0 54.9 1.0
C9 A:RBQ1873 1.3 53.3 1.0
F16 A:RBQ1873 2.1 54.2 1.0
F14 A:RBQ1873 2.1 54.9 1.0
C8 A:RBQ1873 2.4 49.6 1.0
N5 A:RBQ1873 2.9 48.9 1.0
C11 A:RBQ1873 3.0 47.6 1.0
C12 A:RBQ1873 3.1 48.1 1.0
N3 A:RBQ1873 3.2 48.0 1.0
C1 A:RBQ1873 3.2 50.3 1.0
CG A:PRO618 3.6 55.6 1.0
CE A:LYS636 3.8 70.1 1.0
CB A:PRO618 4.0 51.1 1.0
CG2 A:ILE634 4.1 43.7 1.0
CD1 A:ILE634 4.1 44.4 1.0
N2 A:RBQ1873 4.2 51.7 1.0
C6 A:RBQ1873 4.2 49.1 1.0
C18 A:RBQ1873 4.3 48.4 1.0
NZ A:LYS636 4.5 73.9 1.0
O13 A:RBQ1873 4.6 54.6 1.0
CG A:PHE612 4.8 54.0 1.0
CD1 A:PHE612 4.8 56.3 1.0
CD2 A:PHE612 4.9 54.9 1.0
CD A:LYS636 5.0 58.0 1.0
CD A:PRO618 5.0 51.5 1.0

Fluorine binding site 3 out of 3 in 4uwg

Go back to Fluorine Binding Sites List in 4uwg
Fluorine binding site 3 out of 3 in the Discovery of (2S)-8-((3R)-3-Methylmorpholin-4-Yl)-1-(3- Methyl-2-Oxo-Butyl)-2-(Trifluoromethyl)-3,4-Dihydro-2H- Pyrimido(1,2-A)Pyrimidin-6-One: A Novel Potent and Selective Inhibitor of VPS34 For the Treatment of Solid Tumors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Discovery of (2S)-8-((3R)-3-Methylmorpholin-4-Yl)-1-(3- Methyl-2-Oxo-Butyl)-2-(Trifluoromethyl)-3,4-Dihydro-2H- Pyrimido(1,2-A)Pyrimidin-6-One: A Novel Potent and Selective Inhibitor of VPS34 For the Treatment of Solid Tumors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1873

b:54.2
occ:1.00
 F16 A:RBQ1873 0.0 54.2 1.0
C9 A:RBQ1873 1.3 53.3 1.0
F15 A:RBQ1873 2.1 54.9 1.0
F14 A:RBQ1873 2.1 54.9 1.0
C8 A:RBQ1873 2.3 49.6 1.0
N5 A:RBQ1873 2.9 48.9 1.0
CG A:PHE612 3.1 54.0 1.0
CD2 A:PHE612 3.2 54.9 1.0
CB A:PHE612 3.3 53.4 1.0
CG A:PRO618 3.5 55.6 1.0
CD1 A:PHE612 3.6 56.3 1.0
C12 A:RBQ1873 3.7 48.1 1.0
C18 A:RBQ1873 3.7 48.4 1.0
CE2 A:PHE612 3.8 55.3 1.0
C1 A:RBQ1873 4.0 50.3 1.0
CE1 A:PHE612 4.2 58.3 1.0
C21 A:RBQ1873 4.2 48.3 1.0
CZ A:PHE612 4.3 55.6 1.0
CB A:PRO618 4.3 51.1 1.0
C11 A:RBQ1873 4.4 47.6 1.0
CD A:PRO618 4.4 51.5 1.0
CB A:SER614 4.5 65.6 1.0
N3 A:RBQ1873 4.5 48.0 1.0
CA A:PHE612 4.9 52.6 1.0
CD1 A:ILE634 4.9 44.4 1.0
N2 A:RBQ1873 4.9 51.7 1.0

Reference:

B.Pasquier, Y.El-Ahmad, B.Filoche-Romme, C.Dureuil-Sizaire, F.Fassy, P.Abecassis, M.Mathieu, T.Bertrand, T.Benard, C.Barriere, S.El Batti, J.Letallec, V.Sonnefraud, M.Brollo, L.Delbarre, V.Loyau, F.Pilorge, L.Bertin, P.Richepin, J.Arigon, J.Labrosse, J.Clement, F.Durand, R.Combet, P.Perraut, V.Leroy, F.Gay, D.Lefrancois, F.Bretin, J.Marquette, N.Michot, A.Caron, C.Castell, L.Schio, G.Mccort, H.Goulaouic, C.Garcia-Echeverria, B.P.Ronan. Discovery of (2S)-8-[(3R)-3-Methylmorpholin-4-Yl]-1-(3- Methyl-2-Oxo-Butyl)-2-(Trifluoromethyl)-3,4-Dihydro-2H- Pyrimido[1,2-A]Pyrimidin-6-One: A Novel Potent and Selective Inhibitor of VPS34 For the Treatment of Solid Tumors. J.Med.Chem. 2014.
ISSN: ESSN 1520-4804
PubMed: 25402320
DOI: 10.1021/JM5013352
Page generated: Tue Jul 15 01:07:34 2025

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