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Fluorine in PDB 4uwf: 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: 4uwf 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) 34.94 / 2.99
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 87.735, 145.870, 61.343, 90.00, 90.00, 90.00
R / Rfree (%) 21.25 / 24.62

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 4uwf). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 5 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: 4uwf:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine binding site 1 out of 5 in 4uwf

Go back to Fluorine Binding Sites List in 4uwf
Fluorine binding site 1 out of 5 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:F4000

b:31.1
occ:1.00
 F25 A:EUT4000 0.0 31.1 1.0
C5 A:EUT4000 1.3 31.1 1.0
C3 A:EUT4000 2.3 31.1 1.0
C1 A:EUT4000 2.4 30.9 1.0
O A:ASP747 3.4 29.7 1.0
C6 A:EUT4000 3.6 31.1 1.0
C4 A:EUT4000 3.6 30.6 1.0
CG A:PRO689 3.7 36.0 1.0
O A:HOH2068 3.7 16.6 1.0
CB A:PRO689 3.7 31.6 1.0
CD1 A:LEU750 3.8 30.5 1.0
C2 A:EUT4000 4.1 30.7 1.0
CD A:PRO689 4.3 31.5 1.0
C A:ASP747 4.5 30.2 1.0
CD1 A:ILE760 4.6 37.7 1.0
OD1 A:ASP747 4.6 39.8 1.0
CG A:LEU750 4.7 30.5 1.0
F26 A:EUT4000 4.7 31.5 1.0
N20 A:EUT4000 4.8 30.5 1.0
CD2 A:LEU750 4.8 32.9 1.0
CA A:ASP747 4.9 26.2 1.0
CA A:PRO689 5.0 29.9 1.0

Fluorine binding site 2 out of 5 in 4uwf

Go back to Fluorine Binding Sites List in 4uwf
Fluorine binding site 2 out of 5 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:F4000

b:31.5
occ:1.00
 F26 A:EUT4000 0.0 31.5 1.0
C6 A:EUT4000 1.3 31.1 1.0
C2 A:EUT4000 2.3 30.7 1.0
C3 A:EUT4000 2.4 31.1 1.0
CE1 A:PHE612 3.3 36.3 1.0
CE1 A:PHE684 3.6 27.5 1.0
C5 A:EUT4000 3.6 31.1 1.0
C4 A:EUT4000 3.6 30.6 1.0
CD1 A:PHE612 4.0 35.4 1.0
CZ A:PHE684 4.0 26.6 1.0
C1 A:EUT4000 4.1 30.9 1.0
CZ A:PHE612 4.3 35.4 1.0
CD1 A:PHE684 4.7 26.6 1.0
F25 A:EUT4000 4.7 31.1 1.0
N20 A:EUT4000 4.7 30.5 1.0

Fluorine binding site 3 out of 5 in 4uwf

Go back to Fluorine Binding Sites List in 4uwf
Fluorine binding site 3 out of 5 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:F4000

b:31.4
occ:1.00
 F27 A:EUT4000 0.0 31.4 1.0
C18 A:EUT4000 1.4 31.0 1.0
F29 A:EUT4000 2.2 31.0 1.0
F28 A:EUT4000 2.2 31.0 1.0
C17 A:EUT4000 2.4 30.5 1.0
C11 A:EUT4000 2.7 30.2 1.0
C12 A:EUT4000 3.4 29.9 1.0
CB A:SER614 3.6 33.9 1.0
N20 A:EUT4000 3.6 30.5 1.0
CG A:PRO618 3.6 36.7 1.0
OG A:SER614 3.9 42.2 1.0
N22 A:EUT4000 4.4 29.9 1.0
C10 A:EUT4000 4.5 30.0 1.0
C4 A:EUT4000 4.5 30.6 1.0
CD A:PRO618 4.5 32.3 1.0
CB A:PHE612 4.7 30.8 1.0
CB A:PRO618 4.8 32.1 1.0
CG A:PHE612 5.0 32.4 1.0
CA A:SER614 5.0 30.7 1.0

Fluorine binding site 4 out of 5 in 4uwf

Go back to Fluorine Binding Sites List in 4uwf
Fluorine binding site 4 out of 5 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 4 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:F4000

b:31.0
occ:1.00
 F28 A:EUT4000 0.0 31.0 1.0
C18 A:EUT4000 1.4 31.0 1.0
F29 A:EUT4000 2.2 31.0 1.0
F27 A:EUT4000 2.2 31.4 1.0
C17 A:EUT4000 2.4 30.5 1.0
N20 A:EUT4000 2.7 30.5 1.0
C12 A:EUT4000 3.1 29.9 1.0
C11 A:EUT4000 3.1 30.2 1.0
C10 A:EUT4000 3.2 30.0 1.0
N22 A:EUT4000 3.4 29.9 1.0
CG A:PRO618 3.5 36.7 1.0
C4 A:EUT4000 3.8 30.6 1.0
CG2 A:ILE634 4.0 25.7 1.0
CB A:PRO618 4.0 32.1 1.0
CD2 A:PHE612 4.1 34.5 1.0
C2 A:EUT4000 4.2 30.7 1.0
CG A:PHE612 4.2 32.4 1.0
N19 A:EUT4000 4.2 29.5 1.0
CE A:LYS636 4.3 57.9 1.0
CE2 A:PHE612 4.5 37.3 1.0
C9 A:EUT4000 4.5 29.8 1.0
CD1 A:PHE612 4.5 35.4 1.0
CB A:PHE612 4.6 30.8 1.0
CZ A:PHE612 4.8 35.4 1.0
CE1 A:PHE612 4.8 36.3 1.0
CD A:PRO618 4.9 32.3 1.0
NZ A:LYS636 4.9 67.3 1.0
C1 A:EUT4000 4.9 30.9 1.0

Fluorine binding site 5 out of 5 in 4uwf

Go back to Fluorine Binding Sites List in 4uwf
Fluorine binding site 5 out of 5 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 5 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:F4000

b:31.0
occ:1.00
 F29 A:EUT4000 0.0 31.0 1.0
C18 A:EUT4000 1.4 31.0 1.0
F28 A:EUT4000 2.2 31.0 1.0
F27 A:EUT4000 2.2 31.4 1.0
C17 A:EUT4000 2.3 30.5 1.0
N20 A:EUT4000 2.9 30.5 1.0
CG A:PHE612 3.2 32.4 1.0
CD1 A:PHE612 3.3 35.4 1.0
C4 A:EUT4000 3.3 30.6 1.0
CB A:PHE612 3.3 30.8 1.0
C2 A:EUT4000 3.5 30.7 1.0
C11 A:EUT4000 3.7 30.2 1.0
CD2 A:PHE612 4.0 34.5 1.0
CE1 A:PHE612 4.0 36.3 1.0
CG A:PRO618 4.2 36.7 1.0
C10 A:EUT4000 4.2 30.0 1.0
C1 A:EUT4000 4.2 30.9 1.0
C12 A:EUT4000 4.4 29.9 1.0
C6 A:EUT4000 4.5 31.1 1.0
CB A:SER614 4.5 33.9 1.0
CE2 A:PHE612 4.6 37.3 1.0
CZ A:PHE612 4.6 35.4 1.0
N22 A:EUT4000 4.8 29.9 1.0
CA A:PHE612 4.8 29.0 1.0
CD A:PRO618 5.0 32.3 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: Thu Aug 1 06:11:38 2024

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