Fluorine in PDB 5kmn: Trka Jm-Kinase with 1-(2-Methyl-4-Phenyl-Pyrimidin-5-Yl)-3-[[2- (Trifluoromethyl)Phenyl]Methyl]Urea

All present enzymatic activity of Trka Jm-Kinase with 1-(2-Methyl-4-Phenyl-Pyrimidin-5-Yl)-3-[[2- (Trifluoromethyl)Phenyl]Methyl]Urea:
2.7.10.1;

The structure of Trka Jm-Kinase with 1-(2-Methyl-4-Phenyl-Pyrimidin-5-Yl)-3-[[2- (Trifluoromethyl)Phenyl]Methyl]Urea, PDB code: 5kmn was solved by H.P.Su, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.30 / 2.14
Space group	P 31 1 2
Cell size a, b, c (Å), α, β, γ (°)	52.150, 52.150, 228.530, 90.00, 90.00, 120.00
R / Rfree (%)	19.4 / 22.2

The binding sites of Fluorine atom in the Trka Jm-Kinase with 1-(2-Methyl-4-Phenyl-Pyrimidin-5-Yl)-3-[[2- (Trifluoromethyl)Phenyl]Methyl]Urea (pdb code 5kmn). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Trka Jm-Kinase with 1-(2-Methyl-4-Phenyl-Pyrimidin-5-Yl)-3-[[2- (Trifluoromethyl)Phenyl]Methyl]Urea, PDB code: 5kmn:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Trka Jm-Kinase with 1-(2-Methyl-4-Phenyl-Pyrimidin-5-Yl)-3-[[2- (Trifluoromethyl)Phenyl]Methyl]Urea


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Trka Jm-Kinase with 1-(2-Methyl-4-Phenyl-Pyrimidin-5-Yl)-3-[[2- (Trifluoromethyl)Phenyl]Methyl]Urea within 5.0Å range: probe atom residue distance (Å) B Occ A:F901 b:29.2 occ:1.00 F2 A:6UK901 0.0 29.2 1.0 C13 A:6UK901 1.3 28.5 1.0 F1 A:6UK901 2.1 30.0 1.0 F A:6UK901 2.1 30.6 1.0 C12 A:6UK901 2.4 23.2 1.0 C7 A:6UK901 3.1 20.4 1.0 C6 A:6UK901 3.2 21.0 1.0 CD2 A:HIS648 3.3 22.6 1.0 C11 A:6UK901 3.3 21.4 1.0 CG2 A:ILE666 3.3 22.8 1.0 NE2 A:HIS648 3.4 22.1 1.0 O A:HOH1014 3.7 20.0 1.0 CD1 A:LEU641 4.2 30.6 1.0 CB A:ILE666 4.3 22.7 1.0 C8 A:6UK901 4.4 18.0 1.0 CD2 A:LEU476 4.4 36.3 1.0 C A:ILE666 4.4 22.5 1.0 O A:ILE666 4.5 20.9 1.0 N A:GLY667 4.5 19.8 1.0 N3 A:6UK901 4.5 22.4 1.0 CA A:GLY667 4.5 18.8 1.0 C10 A:6UK901 4.6 23.6 1.0 CG A:HIS648 4.6 22.0 1.0 CE1 A:HIS648 4.7 21.8 1.0 CG A:LEU476 4.8 36.9 1.0 C9 A:6UK901 5.0 22.4 1.0 CG2 A:ILE572 5.0 23.9 1.0 CD2 A:LEU567 5.0 57.6 1.0

Fluorine binding site 2 out of 3 in the Trka Jm-Kinase with 1-(2-Methyl-4-Phenyl-Pyrimidin-5-Yl)-3-[[2- (Trifluoromethyl)Phenyl]Methyl]Urea


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Trka Jm-Kinase with 1-(2-Methyl-4-Phenyl-Pyrimidin-5-Yl)-3-[[2- (Trifluoromethyl)Phenyl]Methyl]Urea within 5.0Å range: probe atom residue distance (Å) B Occ A:F901 b:30.6 occ:1.00 F A:6UK901 0.0 30.6 1.0 C13 A:6UK901 1.3 28.5 1.0 F1 A:6UK901 2.1 30.0 1.0 F2 A:6UK901 2.1 29.2 1.0 C12 A:6UK901 2.4 23.2 1.0 C6 A:6UK901 3.0 21.0 1.0 C7 A:6UK901 3.0 20.4 1.0 CG A:LEU476 3.2 36.9 1.0 CD1 A:LEU476 3.4 38.1 1.0 C11 A:6UK901 3.4 21.4 1.0 CD2 A:LEU476 3.5 36.3 1.0 CD2 A:LEU567 3.6 57.6 1.0 C8 A:6UK901 4.3 18.0 1.0 CD2 A:HIS648 4.4 22.6 1.0 N3 A:6UK901 4.4 22.4 1.0 CB A:LEU476 4.6 32.2 1.0 NE2 A:HIS648 4.6 22.1 1.0 CD2 A:LEU564 4.6 38.3 1.0 C10 A:6UK901 4.6 23.6 1.0 CH3 A:ACE0 4.8 33.1 1.0 CD2 A:LEU641 4.8 29.1 1.0 CD1 A:LEU641 4.9 30.6 1.0 C9 A:6UK901 5.0 22.4 1.0

Fluorine binding site 3 out of 3 in the Trka Jm-Kinase with 1-(2-Methyl-4-Phenyl-Pyrimidin-5-Yl)-3-[[2- (Trifluoromethyl)Phenyl]Methyl]Urea


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Trka Jm-Kinase with 1-(2-Methyl-4-Phenyl-Pyrimidin-5-Yl)-3-[[2- (Trifluoromethyl)Phenyl]Methyl]Urea within 5.0Å range: probe atom residue distance (Å) B Occ A:F901 b:30.0 occ:1.00 F1 A:6UK901 0.0 30.0 1.0 C13 A:6UK901 1.3 28.5 1.0 F2 A:6UK901 2.1 29.2 1.0 F A:6UK901 2.1 30.6 1.0 C12 A:6UK901 2.4 23.2 1.0 C11 A:6UK901 2.7 21.4 1.0 CD2 A:LEU567 3.3 57.6 1.0 CG2 A:ILE572 3.4 23.9 1.0 C7 A:6UK901 3.7 20.4 1.0 C10 A:6UK901 4.1 23.6 1.0 CD2 A:LEU641 4.2 29.1 1.0 CD1 A:ILE572 4.3 25.1 1.0 C6 A:6UK901 4.3 21.0 1.0 CD1 A:LEU641 4.4 30.6 1.0 CG A:LEU567 4.4 56.3 1.0 O A:ILE666 4.5 20.9 1.0 CD1 A:LEU476 4.5 38.1 1.0 CB A:ILE572 4.6 25.3 1.0 CG2 A:ILE666 4.7 22.8 1.0 CG1 A:ILE572 4.7 25.8 1.0 C8 A:6UK901 4.8 18.0 1.0 CG A:LEU641 4.8 31.4 1.0 CG A:LEU476 4.8 36.9 1.0 CD2 A:LEU476 4.9 36.3 1.0 C9 A:6UK901 4.9 22.4 1.0 CD2 A:LEU564 4.9 38.3 1.0 CB A:LEU567 4.9 50.9 1.0

H.P.Su, K.Rickert, C.Burlein, K.Narayan, M.Bukhtiyarova, D.M.Hurzy, C.A.Stump, X.Zhang, J.Reid, A.Krasowska-Zoladek, S.Tummala, J.M.Shipman, M.Kornienko, P.A.Lemaire, D.Krosky, A.Heller, A.Achab, C.Chamberlin, P.Saradjian, B.Sauvagnat, X.Yang, M.R.Ziebell, E.Nickbarg, J.M.Sanders, M.T.Bilodeau, S.S.Carroll, K.J.Lumb, S.M.Soisson, D.A.Henze, A.J.Cooke. Structural Characterization of Nonactive Site, Trka-Selective Kinase Inhibitors. Proc. Natl. Acad. Sci. V. 114 E297 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28039433
DOI: 10.1073/PNAS.1611577114