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Fluorine in PDB 5anl: Crystal Structure of VPS34 in Complex with (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, Processed with the Crystaldirect Automated Mounting and Cryo-Cooling Technology

Enzymatic activity of Crystal Structure of VPS34 in Complex with (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, Processed with the Crystaldirect Automated Mounting and Cryo-Cooling Technology

All present enzymatic activity of Crystal Structure of VPS34 in Complex with (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, Processed with the Crystaldirect Automated Mounting and Cryo-Cooling Technology:
2.7.1.137;

Protein crystallography data

The structure of Crystal Structure of VPS34 in Complex with (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, Processed with the Crystaldirect Automated Mounting and Cryo-Cooling Technology, PDB code: 5anl was solved by U.Zander, G.Hoffmann, M.Mathieu, J.-P.Marquette, I.Cornaciu, F.Cipriani, J.A.Marquez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.70
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 88.215, 145.763, 61.474, 90.00, 90.00, 90.00
R / Rfree (%) 20.534 / 26.667

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of VPS34 in Complex with (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, Processed with the Crystaldirect Automated Mounting and Cryo-Cooling Technology (pdb code 5anl). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of VPS34 in Complex with (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, Processed with the Crystaldirect Automated Mounting and Cryo-Cooling Technology, PDB code: 5anl:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 5anl

Go back to Fluorine Binding Sites List in 5anl
Fluorine binding site 1 out of 3 in the Crystal Structure of VPS34 in Complex with (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, Processed with the Crystaldirect Automated Mounting and Cryo-Cooling Technology


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of VPS34 in Complex with (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, Processed with the Crystaldirect Automated Mounting and Cryo-Cooling Technology within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1870

b:40.5
occ:1.00
 F14 A:RBQ1870 0.0 40.5 1.0
C9 A:RBQ1870 1.3 39.7 1.0
F16 A:RBQ1870 2.1 43.1 1.0
F15 A:RBQ1870 2.1 37.9 1.0
C8 A:RBQ1870 2.4 36.2 1.0
N5 A:RBQ1870 2.8 37.2 1.0
C11 A:RBQ1870 2.9 33.4 1.0
C12 A:RBQ1870 2.9 35.1 1.0
N3 A:RBQ1870 3.2 32.8 1.0
C1 A:RBQ1870 3.2 33.5 1.0
CG A:PRO618 3.7 44.2 1.0
C18 A:RBQ1870 3.8 42.9 1.0
CE A:LYS636 3.8 55.9 1.0
CD1 A:ILE634 4.0 44.1 1.0
NZ A:LYS636 4.1 59.5 1.0
CG2 A:ILE634 4.2 36.2 1.0
CB A:PRO618 4.2 42.1 1.0
N2 A:RBQ1870 4.2 30.2 1.0
C6 A:RBQ1870 4.3 34.4 1.0
O13 A:RBQ1870 4.8 39.5 1.0
CD A:LYS636 4.8 50.4 1.0
C21 A:RBQ1870 4.8 49.3 1.0
CG A:LYS636 4.9 45.3 1.0
CD2 A:PHE612 5.0 41.0 1.0
CD A:PRO618 5.0 44.0 1.0

Fluorine binding site 2 out of 3 in 5anl

Go back to Fluorine Binding Sites List in 5anl
Fluorine binding site 2 out of 3 in the Crystal Structure of VPS34 in Complex with (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, Processed with the Crystaldirect Automated Mounting and Cryo-Cooling Technology


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of VPS34 in Complex with (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, Processed with the Crystaldirect Automated Mounting and Cryo-Cooling Technology within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1870

b:37.9
occ:1.00
 F15 A:RBQ1870 0.0 37.9 1.0
C9 A:RBQ1870 1.3 39.7 1.0
F14 A:RBQ1870 2.1 40.5 1.0
F16 A:RBQ1870 2.1 43.1 1.0
C8 A:RBQ1870 2.4 36.2 1.0
N5 A:RBQ1870 2.7 37.2 1.0
C18 A:RBQ1870 2.9 42.9 1.0
CG A:PHE612 3.2 41.7 1.0
CD2 A:PHE612 3.4 41.0 1.0
CG A:PRO618 3.5 44.2 1.0
CD1 A:PHE612 3.6 43.3 1.0
CB A:PHE612 3.6 43.2 1.0
C12 A:RBQ1870 3.7 35.1 1.0
C21 A:RBQ1870 3.8 49.3 1.0
C1 A:RBQ1870 3.8 33.5 1.0
CE2 A:PHE612 3.9 39.6 1.0
CE1 A:PHE612 4.0 41.1 1.0
CZ A:PHE612 4.2 40.0 1.0
CD1 A:ILE634 4.3 44.1 1.0
C11 A:RBQ1870 4.3 33.4 1.0
CB A:PRO618 4.4 42.1 1.0
N3 A:RBQ1870 4.5 32.8 1.0
N2 A:RBQ1870 4.6 30.2 1.0
CD A:PRO618 4.7 44.0 1.0
CG2 A:ILE634 4.9 36.2 1.0
O22 A:RBQ1870 4.9 58.2 1.0

Fluorine binding site 3 out of 3 in 5anl

Go back to Fluorine Binding Sites List in 5anl
Fluorine binding site 3 out of 3 in the Crystal Structure of VPS34 in Complex with (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, Processed with the Crystaldirect Automated Mounting and Cryo-Cooling Technology


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of VPS34 in Complex with (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, Processed with the Crystaldirect Automated Mounting and Cryo-Cooling Technology within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1870

b:43.1
occ:1.00
 F16 A:RBQ1870 0.0 43.1 1.0
C9 A:RBQ1870 1.3 39.7 1.0
F14 A:RBQ1870 2.1 40.5 1.0
F15 A:RBQ1870 2.1 37.9 1.0
C8 A:RBQ1870 2.4 36.2 1.0
C12 A:RBQ1870 2.9 35.1 1.0
CG A:PRO618 3.3 44.2 1.0
N5 A:RBQ1870 3.6 37.2 1.0
C11 A:RBQ1870 3.8 33.4 1.0
CB A:SER614 3.9 64.2 1.0
CD A:PRO618 4.1 44.0 1.0
OG A:SER614 4.2 68.1 1.0
C18 A:RBQ1870 4.3 42.9 1.0
CB A:PRO618 4.5 42.1 1.0
C1 A:RBQ1870 4.5 33.5 1.0
N3 A:RBQ1870 4.6 32.8 1.0
CE A:LYS636 4.7 55.9 1.0
CB A:PHE612 4.7 43.2 1.0
C21 A:RBQ1870 4.8 49.3 1.0
CG A:PHE612 4.9 41.7 1.0

Reference:

U.Zander, G.Hoffmann, I.Cornaciu, J.-P.Marquette, G.Papp, C.Landret, G.Seroul, J.Sinoir, M.Roewer, F.Felisaz, S.Rodriguez-Puente, V.Mariaule, P.Murphy, M.Mathieu, F.Cipriani, J.A.Marquez. Automated Harvesting and Processing of Protein Crystals Through Laser Photoablation. Acta Crystallogr.,Sect.D V. 72 454 2016.
ISSN: ISSN 0907-4449
PubMed: 27050125
DOI: 10.1107/S2059798316000954
Page generated: Thu Aug 1 07:48:12 2024

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