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Fluorine in PDB 4uwk: 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: 4uwk 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) 57.42 / 2.83
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 92.030, 146.930, 61.630, 90.00, 90.00, 90.00
R / Rfree (%) 17.39 / 22.5

Other elements in 4uwk:

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 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

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

Fluorine binding site 1 out of 3 in 4uwk

Go back to Fluorine Binding Sites List in 4uwk
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:51.8
occ:1.00
 F19 A:UJB1872 0.0 51.8 1.0
C18 A:UJB1872 1.3 50.7 1.0
F21 A:UJB1872 2.1 52.3 1.0
F20 A:UJB1872 2.1 49.4 1.0
C1 A:UJB1872 2.4 50.8 1.0
N4 A:UJB1872 2.8 53.2 1.0
C2 A:UJB1872 3.0 48.6 1.0
N3 A:UJB1872 3.2 46.1 1.0
C7 A:UJB1872 3.2 49.2 1.0
C11 A:UJB1872 3.2 50.5 1.0
CE A:LYS636 3.4 69.0 1.0
CG2 A:ILE634 3.6 36.4 1.0
CD1 A:ILE634 3.7 39.5 1.0
N5 A:UJB1872 3.8 45.8 1.0
NZ A:LYS636 4.1 80.2 1.0
C6 A:UJB1872 4.1 44.0 1.0
CG A:PRO618 4.2 52.4 1.0
C28 A:UJB1872 4.3 61.9 1.0
CB A:PRO618 4.4 48.6 1.0
CB A:ILE634 4.6 37.8 1.0
CG1 A:ILE634 4.7 37.8 1.0
CD A:LYS636 4.7 52.5 1.0
O10 A:UJB1872 4.7 48.1 1.0
C8 A:UJB1872 4.7 40.3 1.0
CG A:LYS636 4.8 46.9 1.0
C9 A:UJB1872 4.8 39.4 1.0
C24 A:UJB1872 4.9 71.5 1.0

Fluorine binding site 2 out of 3 in 4uwk

Go back to Fluorine Binding Sites List in 4uwk
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:49.4
occ:1.00
 F20 A:UJB1872 0.0 49.4 1.0
C18 A:UJB1872 1.3 50.7 1.0
F21 A:UJB1872 2.1 52.3 1.0
F19 A:UJB1872 2.1 51.8 1.0
C1 A:UJB1872 2.4 50.8 1.0
C11 A:UJB1872 2.8 50.5 1.0
CG A:PRO618 3.3 52.4 1.0
C7 A:UJB1872 3.5 49.2 1.0
N4 A:UJB1872 3.6 53.2 1.0
CE A:LYS636 3.7 69.0 1.0
OG A:SER614 4.0 66.5 1.0
NZ A:LYS636 4.1 80.2 1.0
CB A:PRO618 4.2 48.6 1.0
CB A:SER614 4.2 56.1 1.0
N3 A:UJB1872 4.3 46.1 1.0
C2 A:UJB1872 4.3 48.6 1.0
CD A:PRO618 4.4 47.9 1.0
C28 A:UJB1872 4.8 61.9 1.0
CD A:LYS636 4.9 52.5 1.0

Fluorine binding site 3 out of 3 in 4uwk

Go back to Fluorine Binding Sites List in 4uwk
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:52.3
occ:1.00
 F21 A:UJB1872 0.0 52.3 1.0
C18 A:UJB1872 1.3 50.7 1.0
F19 A:UJB1872 2.1 51.8 1.0
F20 A:UJB1872 2.1 49.4 1.0
C1 A:UJB1872 2.3 50.8 1.0
N4 A:UJB1872 3.0 53.2 1.0
CG A:PRO618 3.3 52.4 1.0
CG A:PHE612 3.4 48.3 1.0
CB A:PHE612 3.5 46.9 1.0
C11 A:UJB1872 3.7 50.5 1.0
CD2 A:PHE612 3.7 49.7 1.0
CD1 A:PHE612 3.7 50.5 1.0
C2 A:UJB1872 4.0 48.6 1.0
C28 A:UJB1872 4.0 61.9 1.0
CB A:PRO618 4.1 48.6 1.0
C24 A:UJB1872 4.3 71.5 1.0
CD A:PRO618 4.3 47.9 1.0
CE1 A:PHE612 4.4 52.7 1.0
CE2 A:PHE612 4.4 50.4 1.0
CD1 A:ILE634 4.5 39.5 1.0
C7 A:UJB1872 4.5 49.2 1.0
CG2 A:ILE634 4.5 36.4 1.0
CB A:SER614 4.5 56.1 1.0
C23 A:UJB1872 4.6 68.0 1.0
N3 A:UJB1872 4.6 46.1 1.0
CZ A:PHE612 4.7 50.6 1.0
N5 A:UJB1872 4.8 45.8 1.0
OG A:SER614 4.9 66.5 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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