Fluorine in PDB 4p5z: Human EPHA3 Kinase Domain in Complex with Quinoxaline Derivatives

All present enzymatic activity of Human EPHA3 Kinase Domain in Complex with Quinoxaline Derivatives:
2.7.10.1;

The structure of Human EPHA3 Kinase Domain in Complex with Quinoxaline Derivatives, PDB code: 4p5z was solved by J.Dong, A.Caflisch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.02 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.805, 38.235, 75.465, 90.00, 101.46, 90.00
R / Rfree (%)	17.8 / 21.9

The binding sites of Fluorine atom in the Human EPHA3 Kinase Domain in Complex with Quinoxaline Derivatives (pdb code 4p5z). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Human EPHA3 Kinase Domain in Complex with Quinoxaline Derivatives, PDB code: 4p5z:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Human EPHA3 Kinase Domain in Complex with Quinoxaline Derivatives


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human EPHA3 Kinase Domain in Complex with Quinoxaline Derivatives within 5.0Å range: probe atom residue distance (Å) B Occ A:F1001 b:42.8 occ:1.00 F36 A:Q7M1001 0.0 42.8 1.0 C33 A:Q7M1001 1.3 46.7 1.0 F37 A:Q7M1001 1.9 43.6 0.1 F35 A:Q7M1001 2.1 46.0 0.8 C29 A:Q7M1001 2.3 45.8 0.9 H30 A:Q7M1001 2.3 42.2 1.0 C30 A:Q7M1001 2.7 41.7 1.0 HD11 A:LEU737 3.0 40.8 1.0 HD2 A:HIS744 3.1 34.9 1.0 HE2 A:TYR742 3.2 37.6 1.0 HD13 A:LEU737 3.3 40.8 1.0 HE2 A:PHE677 3.5 39.5 1.0 HD21 A:LEU737 3.5 41.0 1.0 C28 A:Q7M1001 3.6 45.4 1.0 CD1 A:LEU737 3.6 40.4 1.0 CE2 A:TYR742 3.7 39.7 1.0 CD2 A:HIS744 3.7 33.3 1.0 HD22 A:LEU737 3.7 41.0 1.0 H28 A:Q7M1001 3.9 45.9 1.0 HG12 A:VAL762 3.9 32.7 1.0 CD2 A:LEU737 4.0 40.5 1.0 C31 A:Q7M1001 4.0 45.2 1.0 CE2 A:PHE677 4.1 40.0 1.0 HD2 A:TYR742 4.1 38.2 1.0 HD2 A:PHE677 4.1 38.5 1.0 HB2 A:ASP764 4.2 43.4 1.0 NE2 A:HIS744 4.2 35.3 1.0 CD2 A:TYR742 4.2 40.2 1.0 HH A:TYR742 4.3 39.5 1.0 HG23 A:ILE682 4.3 31.4 1.0 HG11 A:VAL762 4.3 32.7 1.0 HD12 A:LEU737 4.3 40.8 1.0 CG A:LEU737 4.4 44.9 1.0 CD2 A:PHE677 4.4 39.0 1.0 CZ A:TYR742 4.5 43.5 1.0 CG1 A:VAL762 4.6 32.8 1.0 H31 A:Q7M1001 4.6 45.8 1.0 HG22 A:ILE673 4.6 42.2 1.0 C27 A:Q7M1001 4.7 48.5 0.1 OH A:TYR742 4.7 41.5 1.0 HB A:VAL762 4.8 31.3 1.0 CG A:HIS744 4.8 30.9 1.0 O A:SER763 4.8 35.7 1.0 HG21 A:ILE682 4.8 31.4 1.0 C32 A:Q7M1001 4.8 49.5 1.0 HB3 A:ASP764 4.9 43.4 1.0 HD23 A:LEU737 4.9 41.0 1.0 HG21 A:ILE673 4.9 42.2 1.0 HG A:LEU737 4.9 45.3 1.0 C A:SER763 5.0 35.8 1.0 CB A:ASP764 5.0 45.8 1.0 CZ A:PHE677 5.0 39.2 1.0

Fluorine binding site 2 out of 3 in the Human EPHA3 Kinase Domain in Complex with Quinoxaline Derivatives


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human EPHA3 Kinase Domain in Complex with Quinoxaline Derivatives within 5.0Å range: probe atom residue distance (Å) B Occ A:F1001 b:43.6 occ:0.10 F37 A:Q7M1001 0.0 43.6 0.1 C33 A:Q7M1001 1.2 46.7 1.0 F35 A:Q7M1001 1.9 46.0 0.8 F36 A:Q7M1001 1.9 42.8 1.0 C29 A:Q7M1001 2.2 45.8 0.9 HD2 A:PHE677 2.5 38.5 1.0 HE2 A:PHE677 2.7 39.5 1.0 H30 A:Q7M1001 2.9 42.2 1.0 C30 A:Q7M1001 2.9 41.7 1.0 CD2 A:PHE677 3.0 39.0 1.0 CE2 A:PHE677 3.1 40.0 1.0 C28 A:Q7M1001 3.2 45.4 1.0 H28 A:Q7M1001 3.3 45.9 1.0 HD21 A:LEU737 3.3 41.0 1.0 HG23 A:ILE682 3.4 31.4 1.0 HG21 A:ILE682 3.5 31.4 1.0 HA A:MET674 3.6 42.4 1.0 HG22 A:ILE673 3.8 42.2 1.0 HG2 A:MET674 3.8 48.9 1.0 CG2 A:ILE682 3.9 31.4 1.0 HD22 A:LEU737 4.0 41.0 1.0 HD11 A:LEU737 4.0 40.8 1.0 CD2 A:LEU737 4.1 40.5 1.0 HG22 A:ILE682 4.2 31.4 1.0 C31 A:Q7M1001 4.2 45.2 1.0 CG A:PHE677 4.3 41.7 1.0 CZ A:PHE677 4.4 39.2 1.0 C27 A:Q7M1001 4.4 48.5 0.1 HG22 A:ILE683 4.5 36.9 1.0 HB2 A:PHE677 4.5 38.2 1.0 CA A:MET674 4.5 43.0 1.0 HD13 A:ILE682 4.6 35.2 1.0 HD13 A:LEU737 4.7 40.8 1.0 CG2 A:ILE673 4.7 42.1 1.0 CG A:MET674 4.7 49.5 1.0 CD1 A:LEU737 4.7 40.4 1.0 HE2 A:TYR742 4.7 37.6 1.0 HG21 A:ILE673 4.7 42.2 1.0 HD23 A:LEU737 4.7 41.0 1.0 C32 A:Q7M1001 4.8 49.5 1.0 HZ A:PHE677 4.8 38.7 1.0 HG23 A:ILE683 4.8 36.9 1.0 CB A:PHE677 4.9 38.8 1.0 HG12 A:ILE682 4.9 30.4 1.0 N A:MET674 4.9 41.1 1.0 HG3 A:MET674 4.9 48.9 1.0 H31 A:Q7M1001 4.9 45.8 1.0 CE2 A:TYR742 4.9 39.7 1.0 HD2 A:HIS744 5.0 34.9 1.0

Fluorine binding site 3 out of 3 in the Human EPHA3 Kinase Domain in Complex with Quinoxaline Derivatives


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human EPHA3 Kinase Domain in Complex with Quinoxaline Derivatives within 5.0Å range: probe atom residue distance (Å) B Occ A:F1001 b:46.0 occ:0.78 F35 A:Q7M1001 0.0 46.0 0.8 C33 A:Q7M1001 1.3 46.7 1.0 F37 A:Q7M1001 1.9 43.6 0.1 F36 A:Q7M1001 2.1 42.8 1.0 C29 A:Q7M1001 2.3 45.8 0.9 H28 A:Q7M1001 2.6 45.9 1.0 C28 A:Q7M1001 2.9 45.4 1.0 HG23 A:ILE682 2.9 31.4 1.0 HG22 A:ILE683 3.2 36.9 1.0 HA A:SER763 3.3 37.2 1.0 O A:VAL762 3.4 34.3 1.0 HG12 A:VAL762 3.5 32.7 1.0 C30 A:Q7M1001 3.5 41.7 1.0 CG2 A:ILE682 3.7 31.4 1.0 H30 A:Q7M1001 3.8 42.2 1.0 HD11 A:LEU737 3.8 40.8 1.0 HG21 A:ILE682 3.8 31.4 1.0 C A:VAL762 3.9 32.5 1.0 CA A:SER763 3.9 37.6 1.0 HB A:VAL762 3.9 31.3 1.0 CG2 A:ILE683 4.0 36.9 1.0 HG22 A:ILE682 4.0 31.4 1.0 N A:SER763 4.0 27.8 1.0 C A:SER763 4.0 35.8 1.0 HG21 A:ILE683 4.1 36.9 1.0 HD2 A:PHE677 4.1 38.5 1.0 HD21 A:LEU737 4.1 41.0 1.0 HG23 A:ILE683 4.1 36.9 1.0 H A:ILE683 4.2 33.4 1.0 CG1 A:VAL762 4.3 32.8 1.0 C27 A:Q7M1001 4.3 48.5 0.1 O A:SER763 4.3 35.7 1.0 HG2 A:MET674 4.3 48.9 1.0 HD2 A:HIS744 4.3 34.9 1.0 HG11 A:VAL762 4.4 32.7 1.0 HG12 A:ILE682 4.4 30.4 1.0 CB A:VAL762 4.5 31.4 1.0 HB2 A:ASP764 4.5 43.4 1.0 HE2 A:PHE677 4.5 39.5 1.0 H A:SER763 4.5 27.4 1.0 N A:ASP764 4.6 48.9 1.0 O34 A:Q7M1001 4.6 42.9 0.7 H A:ASP764 4.7 46.5 1.0 C31 A:Q7M1001 4.7 45.2 1.0 CD1 A:LEU737 4.7 40.4 1.0 CD2 A:PHE677 4.7 39.0 1.0 HA A:ILE682 4.8 28.2 1.0 HD13 A:LEU737 4.9 40.8 1.0 CA A:VAL762 4.9 27.2 1.0 N A:ILE683 4.9 33.4 1.0 CD2 A:HIS744 4.9 33.3 1.0 CB A:ILE682 4.9 31.7 1.0 NE2 A:HIS744 4.9 35.3 1.0 CD2 A:LEU737 4.9 40.5 1.0 HA A:MET674 4.9 42.4 1.0 CE2 A:PHE677 5.0 40.0 1.0 C32 A:Q7M1001 5.0 49.5 1.0

A.Unzue, J.Dong, K.Lafleur, H.Zhao, E.Frugier, A.Caflisch, C.Nevado. Pyrrolo[3,2-B]Quinoxaline Derivatives As Types I1/2 and II Eph Tyrosine Kinase Inhibitors: Structure-Based Design, Synthesis, and in Vivo Validation. J.Med.Chem. V. 57 6834 2014.
ISSN: ISSN 0022-2623
PubMed: 25076195
DOI: 10.1021/JM5009242