Fluorine in PDB 1ywn: VEGFR2 in Complex with A Novel 4-Amino-Furo[2,3-D]Pyrimidine

All present enzymatic activity of VEGFR2 in Complex with A Novel 4-Amino-Furo[2,3-D]Pyrimidine:
2.7.1.112;

The structure of VEGFR2 in Complex with A Novel 4-Amino-Furo[2,3-D]Pyrimidine, PDB code: 1ywn was solved by Y.Miyazaki, S.Matsunaga, J.Tang, Y.Maeda, M.Nakano, R.J.Philippe, M.Shibahara, W.Liu, H.Sato, L.Wang, R.T.Nolte, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.89 / 1.71
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	37.953, 95.595, 95.803, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 23

The binding sites of Fluorine atom in the VEGFR2 in Complex with A Novel 4-Amino-Furo[2,3-D]Pyrimidine (pdb code 1ywn). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the VEGFR2 in Complex with A Novel 4-Amino-Furo[2,3-D]Pyrimidine, PDB code: 1ywn:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the VEGFR2 in Complex with A Novel 4-Amino-Furo[2,3-D]Pyrimidine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of VEGFR2 in Complex with A Novel 4-Amino-Furo[2,3-D]Pyrimidine within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:42.7 occ:1.00 F1 A:LIF301 0.0 42.7 1.0 C2 A:LIF301 1.3 37.0 1.0 F3 A:LIF301 2.1 43.3 1.0 F4 A:LIF301 2.1 40.6 1.0 C5 A:LIF301 2.3 35.2 1.0 C6 A:LIF301 3.1 34.9 1.0 C10 A:LIF301 3.2 35.6 1.0 C A:CYS1043 3.3 31.6 1.0 O A:CYS1043 3.5 31.2 1.0 CG2 A:ILE1042 3.5 30.8 1.0 CD2 A:HIS1024 3.6 34.0 1.0 N A:ASP1044 3.6 32.5 1.0 CB A:ASP1044 3.6 35.0 1.0 CA A:CYS1043 3.7 32.0 1.0 NE2 A:HIS1024 3.7 33.4 1.0 O A:ILE1042 4.0 29.2 1.0 N A:CYS1043 4.0 30.9 1.0 C A:ILE1042 4.1 30.3 1.0 CA A:ASP1044 4.2 33.7 1.0 C7 A:LIF301 4.4 33.8 1.0 CD1 A:LEU1017 4.4 32.6 1.0 C9 A:LIF301 4.5 35.8 1.0 CB A:ILE1042 4.6 30.2 1.0 CG A:HIS1024 4.8 34.3 1.0 O14 A:LIF301 4.8 26.6 1.0 C8 A:LIF301 4.9 36.2 1.0 CG A:ASP1044 4.9 36.1 1.0 CE1 A:HIS1024 5.0 37.8 1.0 CA A:ILE1042 5.0 30.6 1.0

Fluorine binding site 2 out of 4 in the VEGFR2 in Complex with A Novel 4-Amino-Furo[2,3-D]Pyrimidine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of VEGFR2 in Complex with A Novel 4-Amino-Furo[2,3-D]Pyrimidine within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:43.3 occ:1.00 F3 A:LIF301 0.0 43.3 1.0 C2 A:LIF301 1.3 37.0 1.0 F4 A:LIF301 2.1 40.6 1.0 F1 A:LIF301 2.1 42.7 1.0 C5 A:LIF301 2.3 35.2 1.0 C10 A:LIF301 2.7 35.6 1.0 CD1 A:LEU1017 3.5 32.6 1.0 C6 A:LIF301 3.6 34.9 1.0 CD2 A:LEU1017 3.7 32.8 1.0 CD1 A:ILE890 3.7 36.8 1.0 C9 A:LIF301 4.1 35.8 1.0 CG A:LEU1017 4.2 31.4 1.0 CD2 A:HIS1024 4.5 34.0 1.0 C7 A:LIF301 4.7 33.8 1.0 CG1 A:VAL896 4.8 34.3 1.0 CG2 A:ILE1042 4.8 30.8 1.0 CB A:ASP1044 4.8 35.0 1.0 C8 A:LIF301 4.9 36.2 1.0 CG1 A:ILE890 4.9 35.4 1.0

Fluorine binding site 3 out of 4 in the VEGFR2 in Complex with A Novel 4-Amino-Furo[2,3-D]Pyrimidine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of VEGFR2 in Complex with A Novel 4-Amino-Furo[2,3-D]Pyrimidine within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:40.6 occ:1.00 F4 A:LIF301 0.0 40.6 1.0 C2 A:LIF301 1.3 37.0 1.0 F3 A:LIF301 2.1 43.3 1.0 F1 A:LIF301 2.1 42.7 1.0 C5 A:LIF301 2.3 35.2 1.0 C6 A:LIF301 2.8 34.9 1.0 CG1 A:VAL896 3.2 34.3 1.0 C10 A:LIF301 3.5 35.6 1.0 O A:ILE1042 3.6 29.2 1.0 C7 A:LIF301 4.2 33.8 1.0 CD1 A:ILE890 4.2 36.8 1.0 C A:ILE1042 4.3 30.3 1.0 CD2 A:LEU1017 4.4 32.8 1.0 CG1 A:VAL897 4.4 36.0 1.0 CG2 A:ILE1042 4.4 30.8 1.0 CB A:VAL896 4.5 32.2 1.0 CD1 A:LEU1017 4.5 32.6 1.0 CA A:CYS1043 4.5 32.0 1.0 C9 A:LIF301 4.6 35.8 1.0 C A:CYS1043 4.7 31.6 1.0 CG2 A:VAL896 4.7 32.8 1.0 N A:CYS1043 4.8 30.9 1.0 N A:VAL897 4.8 31.9 1.0 O14 A:LIF301 4.8 26.6 1.0 N A:ASP1044 4.9 32.5 1.0 C8 A:LIF301 4.9 36.2 1.0 CB A:ILE1042 4.9 30.2 1.0 CD2 A:LEU887 4.9 34.0 1.0 CA A:VAL896 5.0 30.5 1.0 O A:VAL897 5.0 35.6 1.0

Fluorine binding site 4 out of 4 in the VEGFR2 in Complex with A Novel 4-Amino-Furo[2,3-D]Pyrimidine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of VEGFR2 in Complex with A Novel 4-Amino-Furo[2,3-D]Pyrimidine within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:36.5 occ:1.00 F11 A:LIF301 0.0 36.5 1.0 C8 A:LIF301 1.3 36.2 1.0 C7 A:LIF301 2.3 33.8 1.0 C9 A:LIF301 2.4 35.8 1.0 N12 A:LIF301 2.6 32.0 1.0 CG A:GLU883 3.2 32.1 1.0 OE2 A:GLU883 3.2 33.8 1.0 CD A:GLU883 3.3 34.8 1.0 C6 A:LIF301 3.6 34.9 1.0 C10 A:LIF301 3.6 35.6 1.0 C13 A:LIF301 3.9 28.9 1.0 CB A:GLU883 3.9 30.6 1.0 C5 A:LIF301 4.1 35.2 1.0 OE1 A:GLU883 4.1 35.2 1.0 CA A:GLU883 4.2 30.7 1.0 O A:ASP1044 4.4 32.6 1.0 O A:GLU883 4.5 29.4 1.0 N15 A:LIF301 4.6 26.9 1.0 CG A:LEU887 4.7 32.0 1.0 O14 A:LIF301 4.7 26.6 1.0 CB A:ASP1044 4.8 35.0 1.0 C A:GLU883 4.8 30.7 1.0 O A:HOH163 4.8 53.5 1.0 OD2 A:ASP1044 4.8 44.4 1.0 CG2 A:ILE886 4.9 32.4 1.0 CD2 A:LEU887 4.9 34.0 1.0 CD1 A:LEU887 4.9 33.7 1.0

Y.Miyazaki, S.Matsunaga, J.Tang, Y.Maeda, M.Nakano, R.J.Philippe, M.Shibahara, W.Liu, H.Sato, L.Wang, R.T.Nolte. Novel 4-Amino-Furo[2,3-D]Pyrimidines As Tie-2 and VEGFR2 Dual Inhibitors Bioorg.Med.Chem.Lett. V. 15 2203 2005.
ISSN: ISSN 0960-894X
PubMed: 15837294
DOI: 10.1016/J.BMCL.2005.03.034