Fluorine in PDB 2oh4: Crystal Structure of VEGFR2 with A Benzimidazole-Urea Inhibitor

All present enzymatic activity of Crystal Structure of VEGFR2 with A Benzimidazole-Urea Inhibitor:
2.7.10.1;

The structure of Crystal Structure of VEGFR2 with A Benzimidazole-Urea Inhibitor, PDB code: 2oh4 was solved by R.T.Nolte, L.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.67 / 2.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	38.370, 94.250, 95.754, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 23.1

The binding sites of Fluorine atom in the Crystal Structure of VEGFR2 with A Benzimidazole-Urea Inhibitor (pdb code 2oh4). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of VEGFR2 with A Benzimidazole-Urea Inhibitor, PDB code: 2oh4:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Crystal Structure of VEGFR2 with A Benzimidazole-Urea 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 VEGFR2 with A Benzimidazole-Urea Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F303 b:44.5 occ:1.00 F11 A:GIG303 0.0 44.5 1.0 C8 A:GIG303 1.3 41.4 1.0 C7 A:GIG303 2.4 41.1 1.0 C9 A:GIG303 2.4 42.5 1.0 N12 A:GIG303 2.7 39.7 1.0 CG A:GLU883 3.3 51.1 1.0 OE2 A:GLU883 3.3 53.4 1.0 O A:HOH93 3.4 70.5 1.0 CD A:GLU883 3.5 52.1 1.0 C10 A:GIG303 3.6 42.3 1.0 C6 A:GIG303 3.6 41.4 1.0 O A:HOH66 3.7 68.7 1.0 O A:HOH84 3.9 44.8 1.0 O A:HOH153 3.9 65.2 1.0 C13 A:GIG303 4.1 39.2 1.0 C5 A:GIG303 4.1 41.4 1.0 CB A:GLU883 4.1 50.2 1.0 CA A:GLU883 4.5 50.0 1.0 OE1 A:GLU883 4.5 51.2 1.0 CG2 A:ILE886 4.5 52.9 1.0 O A:ASP1044 4.6 56.6 1.0 CD2 A:LEU887 4.6 52.1 1.0 O A:GLU883 4.6 49.7 1.0 CG A:LEU887 4.7 50.9 1.0 N15 A:GIG303 4.7 38.3 1.0 CB A:ILE886 4.9 51.7 1.0 O14 A:GIG303 4.9 36.6 1.0 C A:GLU883 5.0 50.1 1.0 CD1 A:ILE886 5.0 51.5 1.0 CB A:ASP1044 5.0 56.1 1.0

Fluorine binding site 2 out of 4 in the Crystal Structure of VEGFR2 with A Benzimidazole-Urea 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 VEGFR2 with A Benzimidazole-Urea Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F303 b:46.3 occ:1.00 F3 A:GIG303 0.0 46.3 1.0 C2 A:GIG303 1.4 43.4 1.0 F4 A:GIG303 2.1 46.2 1.0 F1 A:GIG303 2.2 44.2 1.0 C5 A:GIG303 2.4 41.4 1.0 C10 A:GIG303 2.8 42.3 1.0 CD1 A:LEU1017 3.4 52.7 1.0 CD2 A:HIS1024 3.5 53.1 1.0 C6 A:GIG303 3.7 41.4 1.0 O A:HOH37 3.9 55.5 1.0 CD2 A:LEU1017 3.9 50.5 1.0 O A:HOH71 4.1 51.7 1.0 C9 A:GIG303 4.2 42.5 1.0 NE2 A:HIS1024 4.2 53.3 1.0 CG A:LEU1017 4.3 51.6 1.0 CG A:HIS1024 4.4 53.1 1.0 CG2 A:ILE1042 4.5 51.6 1.0 CD1 A:ILE890 4.7 56.0 1.0 CB A:HIS1024 4.8 54.0 1.0 C7 A:GIG303 4.8 41.1 1.0 CB A:ASP1044 4.8 56.1 1.0 CA A:HIS1024 4.9 54.3 1.0 O A:CYS1043 5.0 53.3 0.5

Fluorine binding site 3 out of 4 in the Crystal Structure of VEGFR2 with A Benzimidazole-Urea 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 VEGFR2 with A Benzimidazole-Urea Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F303 b:46.2 occ:1.00 F4 A:GIG303 0.0 46.2 1.0 C2 A:GIG303 1.3 43.4 1.0 F3 A:GIG303 2.1 46.3 1.0 F1 A:GIG303 2.1 44.2 1.0 C5 A:GIG303 2.4 41.4 1.0 C6 A:GIG303 2.9 41.4 1.0 C A:CYS1043 3.1 53.1 0.5 C A:CYS1043 3.2 52.9 0.5 O A:CYS1043 3.2 53.3 0.5 CA A:CYS1043 3.3 52.0 0.5 CA A:CYS1043 3.4 52.3 0.5 CD2 A:HIS1024 3.5 53.1 1.0 O A:CYS1043 3.5 53.2 0.5 CG2 A:ILE1042 3.5 51.6 1.0 C10 A:GIG303 3.5 42.3 1.0 NE2 A:HIS1024 3.6 53.3 1.0 N A:ASP1044 3.6 54.0 1.0 N A:CYS1043 3.7 51.1 0.5 N A:CYS1043 3.7 51.3 0.5 O A:ILE1042 3.8 50.4 1.0 C A:ILE1042 3.9 51.0 1.0 CB A:ASP1044 3.9 56.1 1.0 C7 A:GIG303 4.3 41.1 1.0 CA A:ASP1044 4.3 55.9 1.0 CG1 A:VAL897 4.4 58.2 1.0 CD1 A:LEU1017 4.5 52.7 1.0 O14 A:GIG303 4.5 36.6 1.0 CB A:ILE1042 4.5 50.4 1.0 CB A:CYS1043 4.7 52.0 0.5 C9 A:GIG303 4.7 42.5 1.0 CG A:HIS1024 4.7 53.1 1.0 CE1 A:HIS1024 4.8 54.3 1.0 CA A:ILE1042 4.9 50.7 1.0 CB A:CYS1043 4.9 52.4 0.5 O A:HOH71 4.9 51.7 1.0 C8 A:GIG303 5.0 41.4 1.0

Fluorine binding site 4 out of 4 in the Crystal Structure of VEGFR2 with A Benzimidazole-Urea Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of VEGFR2 with A Benzimidazole-Urea Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F303 b:44.2 occ:1.00 F1 A:GIG303 0.0 44.2 1.0 C2 A:GIG303 1.3 43.4 1.0 F4 A:GIG303 2.1 46.2 1.0 F3 A:GIG303 2.2 46.3 1.0 C5 A:GIG303 2.4 41.4 1.0 C6 A:GIG303 3.1 41.4 1.0 C10 A:GIG303 3.5 42.3 1.0 CG1 A:VAL896 3.6 51.5 1.0 CG1 A:VAL897 3.7 58.2 1.0 CD2 A:LEU1017 3.9 50.5 1.0 CD1 A:LEU1017 3.9 52.7 1.0 O A:ILE1042 4.0 50.4 1.0 CD1 A:ILE890 4.3 56.0 1.0 C7 A:GIG303 4.4 41.1 1.0 CG2 A:ILE1042 4.5 51.6 1.0 CG A:LEU1017 4.5 51.6 1.0 C A:ILE1042 4.6 51.0 1.0 CA A:CYS1043 4.6 52.0 0.5 C9 A:GIG303 4.7 42.5 1.0 CB A:VAL896 4.7 50.6 1.0 CG2 A:VAL896 4.8 48.9 1.0 CA A:CYS1043 4.8 52.3 0.5 C A:CYS1043 4.9 53.1 0.5 N A:CYS1043 5.0 51.1 0.5 N A:VAL897 5.0 53.3 1.0 N A:CYS1043 5.0 51.3 0.5 CB A:ILE1042 5.0 50.4 1.0

M.Hasegawa, N.Nishigaki, Y.Washio, K.Kano, P.A.Harris, H.Sato, I.Mori, R.I.West, M.Shibahara, H.Toyoda, L.Wang, R.T.Nolte, J.M.Veal, M.Cheung. Discovery of Novel Benzimidazoles As Potent Inhibitors of Tie-2 and Vegfr-2 Tyrosine Kinase Receptors. J.Med.Chem. V. 50 4453 2007.
ISSN: ISSN 0022-2623
PubMed: 17676829
DOI: 10.1021/JM0611051