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Fluorine in PDB 4uwh: 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: 4uwh 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) 38.60 / 1.93
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 88.825, 145.456, 61.352, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 4uwh:

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:

Sodium (Na) 2 atoms

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

Fluorine binding site 1 out of 3 in 4uwh

Go back to Fluorine Binding Sites List in 4uwh
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:F1876

b:22.9
occ:1.00
 F28 A:JXM1876 0.0 22.9 1.0
C20 A:JXM1876 1.3 22.3 1.0
F29 A:JXM1876 2.2 20.8 1.0
F30 A:JXM1876 2.2 23.9 1.0
C17 A:JXM1876 2.3 20.2 1.0
C11 A:JXM1876 2.8 20.0 1.0
CG A:PRO618 3.4 25.9 1.0
O A:HOH2232 3.4 44.2 1.0
C12 A:JXM1876 3.5 19.3 1.0
O A:HOH2249 3.6 46.1 1.0
N24 A:JXM1876 3.6 19.2 1.0
CB A:SER614 3.9 30.1 1.0
OG A:SER614 4.0 37.8 1.0
CD A:PRO618 4.3 21.5 1.0
C18 A:JXM1876 4.4 20.2 1.0
N23 A:JXM1876 4.4 18.8 1.0
CB A:PRO618 4.5 21.5 1.0
C10 A:JXM1876 4.5 18.2 1.0
CB A:PHE612 4.6 22.9 1.0
CE A:LYS636 4.9 51.6 1.0

Fluorine binding site 2 out of 3 in 4uwh

Go back to Fluorine Binding Sites List in 4uwh
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:F1876

b:20.8
occ:1.00
 F29 A:JXM1876 0.0 20.8 1.0
C20 A:JXM1876 1.4 22.3 1.0
F28 A:JXM1876 2.2 22.9 1.0
F30 A:JXM1876 2.2 23.9 1.0
C17 A:JXM1876 2.4 20.2 1.0
N24 A:JXM1876 2.8 19.2 1.0
C12 A:JXM1876 2.9 19.3 1.0
C11 A:JXM1876 3.0 20.0 1.0
C10 A:JXM1876 3.2 18.2 1.0
N23 A:JXM1876 3.2 18.8 1.0
CE A:LYS636 3.5 51.6 1.0
CG A:PRO618 3.6 25.9 1.0
C18 A:JXM1876 3.8 20.2 1.0
CG2 A:ILE634 3.9 19.5 1.0
NZ A:LYS636 4.0 60.5 1.0
O A:HOH2249 4.0 46.1 1.0
CB A:PRO618 4.1 21.5 1.0
N21 A:JXM1876 4.2 17.9 1.0
C9 A:JXM1876 4.3 18.7 1.0
CD1 A:ILE634 4.5 26.7 1.0
CD2 A:PHE612 4.7 25.5 1.0
CD A:LYS636 4.8 38.5 1.0
CG A:PHE612 4.9 23.9 1.0
O25 A:JXM1876 4.9 20.1 1.0

Fluorine binding site 3 out of 3 in 4uwh

Go back to Fluorine Binding Sites List in 4uwh
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:F1876

b:23.9
occ:1.00
 F30 A:JXM1876 0.0 23.9 1.0
C20 A:JXM1876 1.4 22.3 1.0
F28 A:JXM1876 2.2 22.9 1.0
F29 A:JXM1876 2.2 20.8 1.0
C17 A:JXM1876 2.4 20.2 1.0
N24 A:JXM1876 2.9 19.2 1.0
C18 A:JXM1876 3.0 20.2 1.0
CG A:PHE612 3.0 23.9 1.0
CB A:PHE612 3.2 22.9 1.0
CD1 A:PHE612 3.4 26.4 1.0
CD2 A:PHE612 3.4 25.5 1.0
CG A:PRO618 3.5 25.9 1.0
C11 A:JXM1876 3.7 20.0 1.0
C10 A:JXM1876 4.0 18.2 1.0
C19 A:JXM1876 4.1 21.8 1.0
CE1 A:PHE612 4.1 27.1 1.0
CE2 A:PHE612 4.1 28.1 1.0
C12 A:JXM1876 4.4 19.3 1.0
CB A:PRO618 4.4 21.5 1.0
CZ A:PHE612 4.4 26.0 1.0
O A:HOH2232 4.6 44.2 1.0
N23 A:JXM1876 4.6 18.8 1.0
CD A:PRO618 4.6 21.5 1.0
CA A:PHE612 4.7 21.6 1.0
N21 A:JXM1876 4.9 17.9 1.0
CG2 A:ILE634 4.9 19.5 1.0
CB A:SER614 5.0 30.1 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 06:15:10 2024

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