Fluorine in PDB 3be2: Crystal Structure of the VEGFR2 Kinase Domain in Complex with A Benzamide Inhibitor

All present enzymatic activity of Crystal Structure of the VEGFR2 Kinase Domain in Complex with A Benzamide Inhibitor:
2.7.10.1;

The structure of Crystal Structure of the VEGFR2 Kinase Domain in Complex with A Benzamide Inhibitor, PDB code: 3be2 was solved by D.A.Whittington, J.L.Kim, A.M.Long, Y.Gu, P.Rose, H.Zhao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.00 / 1.75
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.770, 84.380, 47.570, 90.00, 100.09, 90.00
R / Rfree (%)	19.7 / 22.6

The binding sites of Fluorine atom in the Crystal Structure of the VEGFR2 Kinase Domain in Complex with A Benzamide Inhibitor (pdb code 3be2). 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 VEGFR2 Kinase Domain in Complex with A Benzamide Inhibitor, PDB code: 3be2:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of the VEGFR2 Kinase Domain in Complex with A Benzamide Inhibitor


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 VEGFR2 Kinase Domain in Complex with A Benzamide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:22.3 occ:1.00 F2 A:RAJ501 0.0 22.3 1.0 C24 A:RAJ501 1.3 20.7 1.0 F1 A:RAJ501 2.1 22.0 1.0 F3 A:RAJ501 2.1 22.4 1.0 C22 A:RAJ501 2.4 19.2 1.0 C21 A:RAJ501 3.1 19.4 1.0 CD2 A:HIS1026 3.3 17.4 1.0 NE2 A:HIS1026 3.4 17.8 1.0 C23 A:RAJ501 3.4 17.2 1.0 O A:CYS1045 3.6 14.7 1.0 C A:CYS1045 3.6 14.2 1.0 CB A:ASP1046 3.8 16.0 1.0 CG2 A:ILE1044 3.9 15.3 1.0 N A:ASP1046 4.0 15.1 1.0 CA A:CYS1045 4.1 13.5 1.0 O A:HOH79 4.2 24.2 1.0 CD1 A:LEU1019 4.3 14.3 1.0 N A:CYS1045 4.4 13.3 1.0 CA A:ASP1046 4.4 16.8 1.0 CG A:HIS1026 4.4 17.0 1.0 C20 A:RAJ501 4.5 20.2 1.0 CE1 A:HIS1026 4.5 18.2 1.0 O A:ILE1044 4.5 14.3 1.0 C A:ILE1044 4.5 13.6 1.0 C18 A:RAJ501 4.6 17.2 1.0 O A:HOH260 4.8 36.5 1.0 CG A:ASP1046 4.9 17.8 1.0 CB A:ILE1044 4.9 14.3 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of the VEGFR2 Kinase Domain in Complex with A Benzamide Inhibitor


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 VEGFR2 Kinase Domain in Complex with A Benzamide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:22.4 occ:1.00 F3 A:RAJ501 0.0 22.4 1.0 C24 A:RAJ501 1.3 20.7 1.0 F1 A:RAJ501 2.1 22.0 1.0 F2 A:RAJ501 2.1 22.3 1.0 C22 A:RAJ501 2.4 19.2 1.0 C21 A:RAJ501 3.0 19.4 1.0 C23 A:RAJ501 3.6 17.2 1.0 CD1 A:LEU1019 3.8 14.3 1.0 CD2 A:LEU1019 3.9 14.6 1.0 CD1 A:ILE892 4.0 18.7 1.0 CG1 A:VAL898 4.1 15.3 1.0 C20 A:RAJ501 4.4 20.2 1.0 O A:HOH260 4.5 36.5 1.0 CG A:LEU1019 4.5 14.2 1.0 C18 A:RAJ501 4.8 17.2 1.0 CD2 A:LEU889 4.8 16.0 1.0 CD2 A:HIS1026 5.0 17.4 1.0 O A:ILE1044 5.0 14.3 1.0 CG2 A:ILE1044 5.0 15.3 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of the VEGFR2 Kinase Domain in Complex with A Benzamide Inhibitor


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 VEGFR2 Kinase Domain in Complex with A Benzamide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:22.0 occ:1.00 F1 A:RAJ501 0.0 22.0 1.0 C24 A:RAJ501 1.3 20.7 1.0 F2 A:RAJ501 2.1 22.3 1.0 F3 A:RAJ501 2.1 22.4 1.0 C22 A:RAJ501 2.4 19.2 1.0 C23 A:RAJ501 2.8 17.2 1.0 O A:ILE1044 3.0 14.3 1.0 CA A:CYS1045 3.6 13.5 1.0 C A:ILE1044 3.6 13.6 1.0 CG1 A:VAL898 3.7 15.3 1.0 C21 A:RAJ501 3.7 19.4 1.0 N A:CYS1045 3.9 13.3 1.0 C A:CYS1045 3.9 14.2 1.0 CG2 A:ILE1044 4.1 15.3 1.0 C18 A:RAJ501 4.3 17.2 1.0 CG1 A:VAL899 4.3 15.3 1.0 N A:ASP1046 4.3 15.1 1.0 O A:CYS1045 4.4 14.7 1.0 CB A:ILE1044 4.5 14.3 1.0 O1 A:RAJ501 4.5 14.3 1.0 CA A:ILE1044 4.7 13.8 1.0 N A:VAL899 4.8 13.2 1.0 CB A:VAL898 4.8 14.3 1.0 CD1 A:LEU1019 4.8 14.3 1.0 C20 A:RAJ501 4.9 20.2 1.0 CB A:CYS1045 5.0 12.4 1.0 CA A:VAL898 5.0 13.1 1.0

J.C.Harmange, M.M.Weiss, J.Germain, A.J.Polverino, G.Borg, J.Bready, D.Chen, D.Choquette, A.Coxon, T.Demelfi, L.Dipietro, N.Doerr, J.Estrada, J.Flynn, R.F.Graceffa, S.P.Harriman, S.Kaufman, D.S.La, A.Long, M.W.Martin, S.Neervannan, V.F.Patel, M.Potashman, K.Regal, P.M.Roveto, M.L.Schrag, C.Starnes, A.Tasker, Y.Teffera, L.Wang, R.D.White, D.A.Whittington, R.Zanon. Naphthamides As Novel and Potent Vascular Endothelial Growth Factor Receptor Tyrosine Kinase Inhibitors: Design, Synthesis, and Evaluation. J.Med.Chem. V. 51 1649 2008.
ISSN: ISSN 0022-2623
PubMed: 18324761
DOI: 10.1021/JM701097Z