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Fluorine in PDB 4uwl: 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: 4uwl 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) 56.78 / 2.80
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 93.093, 146.357, 61.607, 90.00, 90.00, 90.00
R / Rfree (%) 18.66 / 25.48

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 4uwl). 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: 4uwl:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 4uwl

Go back to Fluorine Binding Sites List in 4uwl
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:F1872

b:36.8
occ:1.00
 F14 A:7A51872 0.0 36.8 1.0
C13 A:7A51872 1.3 37.4 1.0
F15 A:7A51872 2.1 36.6 1.0
F16 A:7A51872 2.1 38.9 1.0
C9 A:7A51872 2.4 38.7 1.0
N8 A:7A51872 2.9 39.7 1.0
C11 A:7A51872 2.9 36.9 1.0
C10 A:7A51872 3.1 38.0 1.0
N6 A:7A51872 3.2 36.9 1.0
C7 A:7A51872 3.2 39.1 1.0
CE A:LYS636 3.7 52.8 1.0
CG A:PRO618 3.7 43.5 1.0
C23 A:7A51872 3.9 39.3 1.0
CD1 A:ILE634 4.1 36.6 1.0
CG2 A:ILE634 4.1 29.1 1.0
CB A:PRO618 4.2 39.6 1.0
N3 A:7A51872 4.2 40.4 1.0
C4 A:7A51872 4.2 38.1 1.0
NZ A:LYS636 4.5 54.8 1.0
O5 A:7A51872 4.7 41.5 1.0
CD A:LYS636 4.9 44.3 1.0
CD2 A:PHE612 4.9 38.4 1.0
CG A:LYS636 4.9 37.3 1.0
CG A:PHE612 5.0 37.0 1.0
C2 A:7A51872 5.0 37.8 1.0

Fluorine binding site 2 out of 3 in 4uwl

Go back to Fluorine Binding Sites List in 4uwl
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:F1872

b:36.6
occ:1.00
 F15 A:7A51872 0.0 36.6 1.0
C13 A:7A51872 1.3 37.4 1.0
F14 A:7A51872 2.1 36.8 1.0
F16 A:7A51872 2.1 38.9 1.0
C9 A:7A51872 2.4 38.7 1.0
N8 A:7A51872 2.9 39.7 1.0
C23 A:7A51872 3.1 39.3 1.0
CG A:PHE612 3.2 37.0 1.0
CB A:PHE612 3.3 36.4 1.0
CG A:PRO618 3.4 43.5 1.0
CD1 A:PHE612 3.6 38.2 1.0
CD2 A:PHE612 3.7 38.4 1.0
O2 A:SO41871 3.7 93.9 1.0
C10 A:7A51872 3.7 38.0 1.0
C7 A:7A51872 4.0 39.1 1.0
O4 A:SO41871 4.2 93.4 1.0
CB A:PRO618 4.3 39.6 1.0
CE1 A:PHE612 4.3 38.1 1.0
CB A:SER614 4.3 46.4 1.0
C11 A:7A51872 4.4 36.9 1.0
CE2 A:PHE612 4.4 40.2 1.0
S A:SO41871 4.4 94.0 1.0
CD A:PRO618 4.4 39.5 1.0
C24 A:7A51872 4.5 41.8 1.0
N6 A:7A51872 4.5 36.9 1.0
CD1 A:ILE634 4.6 36.6 1.0
O3 A:SO41871 4.7 93.0 1.0
CZ A:PHE612 4.7 37.4 1.0
N3 A:7A51872 4.8 40.4 1.0
CA A:PHE612 4.8 35.6 1.0
OG A:SER614 4.9 53.6 1.0

Fluorine binding site 3 out of 3 in 4uwl

Go back to Fluorine Binding Sites List in 4uwl
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:F1872

b:38.9
occ:1.00
 F16 A:7A51872 0.0 38.9 1.0
C13 A:7A51872 1.3 37.4 1.0
F15 A:7A51872 2.1 36.6 1.0
F14 A:7A51872 2.1 36.8 1.0
C9 A:7A51872 2.4 38.7 1.0
C10 A:7A51872 2.9 38.0 1.0
CG A:PRO618 3.3 43.5 1.0
OG A:SER614 3.4 53.6 1.0
CB A:SER614 3.5 46.4 1.0
C11 A:7A51872 3.6 36.9 1.0
N8 A:7A51872 3.7 39.7 1.0
CD A:PRO618 4.2 39.5 1.0
O2 A:SO41871 4.2 93.9 1.0
CB A:PRO618 4.4 39.6 1.0
N6 A:7A51872 4.5 36.9 1.0
C7 A:7A51872 4.5 39.1 1.0
C23 A:7A51872 4.5 39.3 1.0
O4 A:SO41871 4.6 93.4 1.0
CB A:PHE612 4.8 36.4 1.0
CE A:LYS636 4.8 52.8 1.0
CA A:SER614 5.0 43.7 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 01:08:01 2025

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