Fluorine in PDB 5fza: Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with 3D Fragment 2-Piperidin-4-Yloxy-5-(Trifluoromethyl)Pyridine (N10072A) (Ligand Modelled Based on Pandda Event Map)

The structure of Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with 3D Fragment 2-Piperidin-4-Yloxy-5-(Trifluoromethyl)Pyridine (N10072A) (Ligand Modelled Based on Pandda Event Map), PDB code: 5fza was solved by R.Nowak, T.Krojer, N.Pearce, C.Johansson, C.Gileadi, K.Kupinska, C.Strain-Damerell, A.Szykowska, N.A.Burgess-Brown, C.H.Arrowsmith, C.Bountra, A.M.Edwards, F.Von Delft, P.E.Brennan, U.Oppermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.71 / 2.10
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	141.370, 141.370, 153.105, 90.00, 90.00, 120.00
R / Rfree (%)	19.3 / 22.8

The structure of Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with 3D Fragment 2-Piperidin-4-Yloxy-5-(Trifluoromethyl)Pyridine (N10072A) (Ligand Modelled Based on Pandda Event Map) also contains other interesting chemical elements:

Manganese	(Mn)	1 atom
Zinc	(Zn)	2 atoms
Chlorine	(Cl)	1 atom

The binding sites of Fluorine atom in the Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with 3D Fragment 2-Piperidin-4-Yloxy-5-(Trifluoromethyl)Pyridine (N10072A) (Ligand Modelled Based on Pandda Event Map) (pdb code 5fza). 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 the Catalytic Domain of Human JARID1B in Complex with 3D Fragment 2-Piperidin-4-Yloxy-5-(Trifluoromethyl)Pyridine (N10072A) (Ligand Modelled Based on Pandda Event Map), PDB code: 5fza:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with 3D Fragment 2-Piperidin-4-Yloxy-5-(Trifluoromethyl)Pyridine (N10072A) (Ligand Modelled Based on Pandda Event Map)


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 the Catalytic Domain of Human JARID1B in Complex with 3D Fragment 2-Piperidin-4-Yloxy-5-(Trifluoromethyl)Pyridine (N10072A) (Ligand Modelled Based on Pandda Event Map) within 5.0Å range: probe atom residue distance (Å) B Occ A:F1758 b:46.9 occ:0.63 F15 A:80Q1758 0.0 46.9 0.6 C14 A:80Q1758 1.4 47.5 0.6 F17 A:80Q1758 2.2 46.1 0.6 F16 A:80Q1758 2.2 45.3 0.6 C11 A:80Q1758 2.3 43.5 0.6 C12 A:80Q1758 3.0 44.4 0.6 NH2 A:ARG666 3.1 37.4 1.0 CE A:MET701 3.1 26.9 1.0 C10 A:80Q1758 3.4 40.8 0.6 CG A:GLU662 3.5 29.7 1.0 CZ A:ARG666 3.6 41.1 1.0 O A:HOH2218 3.6 32.1 1.0 CD1 A:LEU741 3.6 49.6 1.0 O A:TYR736 3.6 27.1 1.0 NH1 A:ARG666 4.1 48.3 1.0 NE A:ARG666 4.2 41.4 1.0 N13 A:80Q1758 4.3 43.1 0.6 CB A:GLU662 4.3 29.4 1.0 C A:TYR736 4.4 34.0 1.0 CG A:LEU741 4.4 43.3 1.0 CB A:TYR736 4.5 26.2 1.0 CD A:GLU662 4.6 35.3 1.0 C09 A:80Q1758 4.6 39.3 0.6 SD A:MET701 4.6 36.0 1.0 O A:THR737 4.6 29.9 1.0 C A:THR737 4.6 37.5 1.0 OE2 A:GLU662 4.7 31.4 1.0 N A:LEU738 4.9 42.1 1.0 C08 A:80Q1758 4.9 45.9 0.6 CA A:TYR736 4.9 30.2 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with 3D Fragment 2-Piperidin-4-Yloxy-5-(Trifluoromethyl)Pyridine (N10072A) (Ligand Modelled Based on Pandda Event Map)


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 the Catalytic Domain of Human JARID1B in Complex with 3D Fragment 2-Piperidin-4-Yloxy-5-(Trifluoromethyl)Pyridine (N10072A) (Ligand Modelled Based on Pandda Event Map) within 5.0Å range: probe atom residue distance (Å) B Occ A:F1758 b:45.3 occ:0.63 F16 A:80Q1758 0.0 45.3 0.6 C14 A:80Q1758 1.4 47.5 0.6 F17 A:80Q1758 2.2 46.1 0.6 F15 A:80Q1758 2.2 46.9 0.6 C11 A:80Q1758 2.3 43.5 0.6 C10 A:80Q1758 2.6 40.8 0.6 CG A:GLU662 3.6 29.7 1.0 CB A:GLU662 3.6 29.4 1.0 CD1 A:LEU741 3.6 49.6 1.0 C12 A:80Q1758 3.7 44.4 0.6 CG2 A:ILE659 3.8 33.8 1.0 CA A:ILE659 3.8 32.3 1.0 O A:ILE659 3.8 29.8 1.0 CE A:MET701 3.9 26.9 1.0 CD2 A:LEU738 3.9 48.0 1.0 CG1 A:ILE659 4.0 27.1 1.0 CB A:ILE659 4.0 31.3 1.0 C09 A:80Q1758 4.1 39.3 0.6 C A:ILE659 4.2 30.4 1.0 N A:LYS663 4.6 31.1 1.0 CG A:LEU741 4.8 43.3 1.0 CG A:LEU738 4.8 50.1 1.0 CA A:GLU662 4.8 32.5 1.0 N13 A:80Q1758 4.8 43.1 0.6 C A:GLU662 4.8 34.6 1.0 N A:ILE659 4.9 30.6 1.0 C08 A:80Q1758 4.9 45.9 0.6 O A:MET658 4.9 29.2 1.0 NH2 A:ARG666 5.0 37.4 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with 3D Fragment 2-Piperidin-4-Yloxy-5-(Trifluoromethyl)Pyridine (N10072A) (Ligand Modelled Based on Pandda Event Map)


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 the Catalytic Domain of Human JARID1B in Complex with 3D Fragment 2-Piperidin-4-Yloxy-5-(Trifluoromethyl)Pyridine (N10072A) (Ligand Modelled Based on Pandda Event Map) within 5.0Å range: probe atom residue distance (Å) B Occ A:F1758 b:46.1 occ:0.63 F17 A:80Q1758 0.0 46.1 0.6 C14 A:80Q1758 1.3 47.5 0.6 F15 A:80Q1758 2.2 46.9 0.6 F16 A:80Q1758 2.2 45.3 0.6 C11 A:80Q1758 2.3 43.5 0.6 C12 A:80Q1758 2.9 44.4 0.6 CD1 A:LEU741 3.0 49.6 1.0 CA A:LEU738 3.3 43.4 1.0 C10 A:80Q1758 3.4 40.8 0.6 CD2 A:LEU738 3.4 48.0 1.0 N A:LEU738 3.4 42.1 1.0 O A:THR737 3.4 29.9 1.0 CG A:LEU741 3.5 43.3 1.0 C A:THR737 3.5 37.5 1.0 CG A:LEU738 3.8 50.1 1.0 CB A:LEU741 4.0 37.8 1.0 CB A:LEU738 4.1 50.8 1.0 N13 A:80Q1758 4.2 43.1 0.6 O A:TYR736 4.4 27.1 1.0 C A:LEU738 4.4 49.2 1.0 C09 A:80Q1758 4.6 39.3 0.6 CA A:THR737 4.6 37.3 1.0 O A:LEU738 4.6 54.1 1.0 CG2 A:ILE659 4.7 33.8 1.0 CE A:MET701 4.7 26.9 1.0 C A:TYR736 4.7 34.0 1.0 CB A:TYR736 4.8 26.2 1.0 C08 A:80Q1758 4.9 45.9 0.6 CG1 A:ILE659 4.9 27.1 1.0 CD2 A:LEU741 4.9 40.5 1.0 NH2 A:ARG666 4.9 37.4 1.0 N A:THR737 5.0 28.9 1.0

R.Nowak, T.Krojer, N.Pearce, C.Johansson, C.Gileadi, K.Kupinska, C.Strain-Damerell, A.Szykowska, N.A.Burgess-Brown, C.H.Arrowsmith, C.Bountra, A.M.Edwards, F.Von Delft, P.E.Brennan, U.Oppermann. Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with 3D Fragment 2-Piperidin-4-Yloxy-5-(Trifluoromethyl)Pyridine (N10072A) (Ligand Modelled Based on Pandda Event Map) To Be Published.