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Sodium 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:

Fluorine (F) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium 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 Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4uwh

Go back to Sodium Binding Sites List in 4uwh
Sodium binding site 1 out of 2 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 Sodium with other atoms in the Na 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:Na1874

b:32.7
occ:1.00
 O A:HOH2273 2.2 35.2 1.0
O A:LEU667 2.3 17.2 1.0
O A:HOH2272 2.4 25.8 1.0
O A:HOH2280 2.5 30.3 1.0
O A:HOH2271 2.6 17.8 1.0
C A:LEU667 3.4 18.1 1.0
NH2 A:ARG659 3.4 48.3 1.0
N A:LEU667 3.4 14.4 1.0
C A:LYS666 3.8 18.6 1.0
CA A:LEU667 3.9 14.4 1.0
NZ A:LYS756 4.0 55.4 1.0
CA A:LYS666 4.1 15.5 1.0
CE A:LYS756 4.1 49.7 1.0
CD A:PRO669 4.3 18.7 1.0
OD1 A:ASP664 4.4 28.2 1.0
OD2 A:ASP655 4.4 27.7 1.0
OD1 A:ASP655 4.5 23.1 1.0
N A:THR668 4.5 15.1 1.0
O A:HOH2179 4.5 42.6 1.0
CZ A:ARG659 4.5 61.2 1.0
O A:HOH2322 4.6 36.1 1.0
O A:LYS666 4.6 18.1 1.0
CB A:LEU667 4.6 14.5 1.0
CG A:ASP655 4.8 23.7 1.0
NE A:ARG659 4.8 45.0 1.0
N A:LYS666 4.8 16.3 1.0
CA A:THR668 4.9 15.1 1.0

Sodium binding site 2 out of 2 in 4uwh

Go back to Sodium Binding Sites List in 4uwh
Sodium binding site 2 out of 2 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 Sodium with other atoms in the Na 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:Na1875

b:22.4
occ:1.00
 O A:GLU439 2.2 26.7 1.0
O A:HOH2128 2.3 17.8 1.0
O A:HOH2119 2.3 21.7 1.0
O A:HOH2117 2.9 40.3 1.0
C A:GLU439 3.4 27.9 1.0
OE1 A:GLN444 4.0 24.7 1.0
N A:ASP441 4.1 19.7 1.0
CA A:GLU439 4.2 26.4 1.0
N A:ILE440 4.3 23.3 1.0
CA A:ILE440 4.4 22.5 1.0
CB A:ASP441 4.6 20.7 1.0
CG A:GLU439 4.7 41.6 1.0
C A:ILE440 4.7 25.1 1.0
CB A:GLU439 4.8 28.0 1.0
CA A:ASP441 5.0 19.1 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: Mon Oct 7 18:46:48 2024

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