Fluorine in PDB 3ewh: Crystal Structure of the VEGFR2 Kinase Domain in Complex with A Pyridyl-Pyrimidine Benzimidazole Inhibitor

All present enzymatic activity of Crystal Structure of the VEGFR2 Kinase Domain in Complex with A Pyridyl-Pyrimidine Benzimidazole Inhibitor:
2.7.10.1;

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

Resolution Low / High (Å)	21.10 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.319, 84.380, 47.404, 90.00, 99.33, 90.00
R / Rfree (%)	20.6 / 23.4

The binding sites of Fluorine atom in the Crystal Structure of the VEGFR2 Kinase Domain in Complex with A Pyridyl-Pyrimidine Benzimidazole Inhibitor (pdb code 3ewh). 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 Pyridyl-Pyrimidine Benzimidazole Inhibitor, PDB code: 3ewh:
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 Pyridyl-Pyrimidine Benzimidazole 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 Pyridyl-Pyrimidine Benzimidazole Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:24.0 occ:1.00 F2 A:K111 0.0 24.0 1.0 C39 A:K111 1.3 20.2 1.0 F1 A:K111 2.2 24.1 1.0 F3 A:K111 2.2 22.8 1.0 C9 A:K111 2.3 19.4 1.0 C8 A:K111 2.8 18.5 1.0 CD2 A:HIS1026 3.3 15.3 1.0 C10 A:K111 3.5 18.6 1.0 CD1 A:LEU1019 3.5 15.7 1.0 CG2 A:ILE1044 3.7 14.2 1.0 NE2 A:HIS1026 3.7 15.7 1.0 C7 A:K111 4.2 18.8 1.0 CG A:HIS1026 4.4 14.8 1.0 C A:CYS1045 4.5 16.0 1.0 CD2 A:LEU1019 4.5 14.4 1.0 O A:CYS1045 4.5 15.2 1.0 O A:ILE1044 4.6 14.0 1.0 C11 A:K111 4.6 19.0 1.0 CG A:LEU1019 4.6 15.4 1.0 CA A:CYS1045 4.6 15.7 1.0 CB A:ILE1044 4.7 13.1 1.0 C A:ILE1044 4.7 13.7 1.0 N A:ASP1046 4.8 17.1 1.0 CG1 A:VAL898 4.8 16.4 1.0 N A:CYS1045 4.9 14.5 1.0 CE1 A:HIS1026 4.9 16.4 1.0 C6 A:K111 4.9 19.3 1.0 CB A:ASP1046 4.9 18.9 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of the VEGFR2 Kinase Domain in Complex with A Pyridyl-Pyrimidine Benzimidazole 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 Pyridyl-Pyrimidine Benzimidazole Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:22.8 occ:1.00 F3 A:K111 0.0 22.8 1.0 C39 A:K111 1.3 20.2 1.0 F1 A:K111 2.2 24.1 1.0 F2 A:K111 2.2 24.0 1.0 C9 A:K111 2.4 19.4 1.0 C10 A:K111 2.7 18.6 1.0 CD1 A:ILE892 3.6 18.9 1.0 CD2 A:LEU1019 3.6 14.4 1.0 C8 A:K111 3.7 18.5 1.0 CD1 A:LEU1019 3.7 15.7 1.0 C11 A:K111 4.1 19.0 1.0 CG A:LEU1019 4.3 15.4 1.0 CD2 A:HIS1026 4.8 15.3 1.0 C7 A:K111 4.8 18.8 1.0 CG1 A:ILE892 4.9 18.2 1.0 C6 A:K111 4.9 19.3 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of the VEGFR2 Kinase Domain in Complex with A Pyridyl-Pyrimidine Benzimidazole 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 Pyridyl-Pyrimidine Benzimidazole Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:24.1 occ:1.00 F1 A:K111 0.0 24.1 1.0 C39 A:K111 1.3 20.2 1.0 F2 A:K111 2.2 24.0 1.0 F3 A:K111 2.2 22.8 1.0 C9 A:K111 2.3 19.4 1.0 C8 A:K111 3.0 18.5 1.0 CG1 A:VAL898 3.2 16.4 1.0 C10 A:K111 3.3 18.6 1.0 CD2 A:LEU1019 3.4 14.4 1.0 CD1 A:LEU1019 3.7 15.7 1.0 CD1 A:ILE892 4.0 18.9 1.0 CG A:LEU1019 4.2 15.4 1.0 C7 A:K111 4.3 18.8 1.0 CB A:VAL898 4.4 15.1 1.0 CG2 A:VAL898 4.4 15.2 1.0 C11 A:K111 4.5 19.0 1.0 O A:ILE1044 4.6 14.0 1.0 CG2 A:ILE892 4.9 18.8 1.0 C6 A:K111 4.9 19.3 1.0 CG2 A:ILE1044 4.9 14.2 1.0 CD2 A:LEU889 5.0 15.9 1.0

V.J.Cee, A.C.Cheng, K.Romero, S.Bellon, C.Mohr, D.A.Whittington, A.Bak, J.Bready, S.Caenepeel, A.Coxon, H.L.Deak, J.Fretland, Y.Gu, B.L.Hodous, X.Huang, J.L.Kim, J.Lin, A.M.Long, H.Nguyen, P.R.Olivieri, V.F.Patel, L.Wang, Y.Zhou, P.Hughes, S.Geuns-Meyer. Pyridyl-Pyrimidine Benzimidazole Derivatives As Potent, Selective, and Orally Bioavailable Inhibitors of Tie-2 Kinase. Bioorg.Med.Chem.Lett. V. 19 424 2009.
ISSN: ISSN 0960-894X
PubMed: 19062275
DOI: 10.1016/J.BMCL.2008.11.056