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

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

The structure of Trka Jm-Kinase with 1-(5-Methyl-3-Phenyl-1,2-Oxazol-4-Yl)-3-[[2- (Trifluoromethyl)Phenyl]Methyl]Urea, PDB code: 5kml 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)	22.89 / 2.01
Space group	P 31 1 2
Cell size a, b, c (Å), α, β, γ (°)	51.920, 51.920, 230.960, 90.00, 90.00, 120.00
R / Rfree (%)	20.2 / 23.2

The binding sites of Fluorine atom in the Trka Jm-Kinase with 1-(5-Methyl-3-Phenyl-1,2-Oxazol-4-Yl)-3-[[2- (Trifluoromethyl)Phenyl]Methyl]Urea (pdb code 5kml). 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-(5-Methyl-3-Phenyl-1,2-Oxazol-4-Yl)-3-[[2- (Trifluoromethyl)Phenyl]Methyl]Urea, PDB code: 5kml:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Trka Jm-Kinase with 1-(5-Methyl-3-Phenyl-1,2-Oxazol-4-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-(5-Methyl-3-Phenyl-1,2-Oxazol-4-Yl)-3-[[2- (Trifluoromethyl)Phenyl]Methyl]Urea within 5.0Å range: probe atom residue distance (Å) B Occ A:F901 b:34.5 occ:1.00 F2 A:6UH901 0.0 34.5 1.0 C18 A:6UH901 1.3 35.2 1.0 F A:6UH901 2.1 37.6 1.0 F1 A:6UH901 2.1 35.9 1.0 C17 A:6UH901 2.4 30.5 1.0 C16 A:6UH901 2.7 28.5 1.0 CD2 A:LEU567 3.0 62.3 1.0 CG2 A:ILE572 3.6 26.7 1.0 C12 A:6UH901 3.7 27.5 1.0 C15 A:6UH901 4.1 27.6 1.0 CD2 A:LEU641 4.2 34.4 1.0 CD1 A:ILE572 4.2 34.9 1.0 C11 A:6UH901 4.3 27.3 1.0 CG A:LEU567 4.3 58.6 1.0 CD1 A:LEU641 4.4 34.8 1.0 CD1 A:LEU476 4.5 44.4 1.0 CG2 A:ILE666 4.6 26.9 1.0 O A:ILE666 4.7 23.6 1.0 C13 A:6UH901 4.8 23.6 1.0 CG1 A:ILE572 4.8 28.8 1.0 CB A:ILE572 4.8 27.7 1.0 CB A:LEU567 4.8 53.0 1.0 CG A:LEU476 4.9 43.8 1.0 CD2 A:LEU476 4.9 43.5 1.0 CG A:LEU641 4.9 35.2 1.0 C14 A:6UH901 4.9 25.9 1.0 CD2 A:HIS648 5.0 24.1 1.0

Fluorine binding site 2 out of 3 in the Trka Jm-Kinase with 1-(5-Methyl-3-Phenyl-1,2-Oxazol-4-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-(5-Methyl-3-Phenyl-1,2-Oxazol-4-Yl)-3-[[2- (Trifluoromethyl)Phenyl]Methyl]Urea within 5.0Å range: probe atom residue distance (Å) B Occ A:F901 b:37.6 occ:1.00 F A:6UH901 0.0 37.6 1.0 C18 A:6UH901 1.3 35.2 1.0 F2 A:6UH901 2.1 34.5 1.0 F1 A:6UH901 2.1 35.9 1.0 C17 A:6UH901 2.4 30.5 1.0 C11 A:6UH901 3.0 27.3 1.0 C12 A:6UH901 3.0 27.5 1.0 CG A:LEU476 3.3 43.8 1.0 CD1 A:LEU476 3.3 44.4 1.0 C16 A:6UH901 3.4 28.5 1.0 CD2 A:LEU567 3.5 62.3 1.0 CD2 A:LEU476 3.7 43.5 1.0 C13 A:6UH901 4.3 23.6 1.0 N2 A:6UH901 4.4 30.3 1.0 CD2 A:HIS648 4.4 24.1 1.0 C15 A:6UH901 4.6 27.6 1.0 NE2 A:HIS648 4.6 24.1 1.0 CB A:LEU476 4.7 39.9 1.0 CD2 A:LEU564 4.7 39.2 1.0 CH3 A:ACE0 4.9 47.9 1.0 CD2 A:LEU641 5.0 34.4 1.0 CG A:LEU567 5.0 58.6 1.0 C14 A:6UH901 5.0 25.9 1.0

Fluorine binding site 3 out of 3 in the Trka Jm-Kinase with 1-(5-Methyl-3-Phenyl-1,2-Oxazol-4-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-(5-Methyl-3-Phenyl-1,2-Oxazol-4-Yl)-3-[[2- (Trifluoromethyl)Phenyl]Methyl]Urea within 5.0Å range: probe atom residue distance (Å) B Occ A:F901 b:35.9 occ:1.00 F1 A:6UH901 0.0 35.9 1.0 C18 A:6UH901 1.3 35.2 1.0 F2 A:6UH901 2.1 34.5 1.0 F A:6UH901 2.1 37.6 1.0 C17 A:6UH901 2.4 30.5 1.0 C12 A:6UH901 3.1 27.5 1.0 CD2 A:HIS648 3.2 24.1 1.0 C11 A:6UH901 3.2 27.3 1.0 NE2 A:HIS648 3.3 24.1 1.0 C16 A:6UH901 3.4 28.5 1.0 CG2 A:ILE666 3.5 26.9 1.0 O A:HOH1018 3.5 20.1 1.0 CD1 A:LEU641 4.3 34.8 1.0 C13 A:6UH901 4.4 23.6 1.0 N2 A:6UH901 4.4 30.3 1.0 CG A:HIS648 4.4 23.9 1.0 CE1 A:HIS648 4.5 23.4 1.0 C15 A:6UH901 4.6 27.6 1.0 CD2 A:LEU476 4.6 43.5 1.0 CB A:ILE666 4.6 25.6 1.0 N A:GLY667 4.6 21.7 1.0 C A:ILE666 4.6 25.7 1.0 CA A:GLY667 4.6 20.8 1.0 O A:ILE666 4.7 23.6 1.0 CD2 A:LEU567 4.8 62.3 1.0 CG A:LEU476 4.9 43.8 1.0 C14 A:6UH901 5.0 25.9 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