Fluorine in PDB 6fni: Crystal Structure of Ephrin B4 (EPHB4) Receptor Protein Kinase with Nvp-BHG712

All present enzymatic activity of Crystal Structure of Ephrin B4 (EPHB4) Receptor Protein Kinase with Nvp-BHG712:
2.7.10.1;

The structure of Crystal Structure of Ephrin B4 (EPHB4) Receptor Protein Kinase with Nvp-BHG712, PDB code: 6fni was solved by D.Kudlinzki, A.Troester, K.Witt, V.L.Linhard, K.Saxena, H.Schwalbe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.46 / 1.47
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	114.215, 114.215, 53.192, 90.00, 90.00, 120.00
R / Rfree (%)	22.4 / 23.6

The binding sites of Fluorine atom in the Crystal Structure of Ephrin B4 (EPHB4) Receptor Protein Kinase with Nvp-BHG712 (pdb code 6fni). 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 Ephrin B4 (EPHB4) Receptor Protein Kinase with Nvp-BHG712, PDB code: 6fni:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of Ephrin B4 (EPHB4) Receptor Protein Kinase with Nvp-BHG712


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 Ephrin B4 (EPHB4) Receptor Protein Kinase with Nvp-BHG712 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1001 b:30.4 occ:1.00 F18 A:DXH1001 0.0 30.4 1.0 C17 A:DXH1001 1.4 32.0 1.0 F19 A:DXH1001 2.2 29.8 1.0 F20 A:DXH1001 2.2 29.6 1.0 C15 A:DXH1001 2.3 35.8 1.0 C14 A:DXH1001 2.7 34.8 1.0 CE1 A:PHE671 3.5 38.7 1.0 CE2 A:TYR736 3.5 24.0 1.0 C16 A:DXH1001 3.6 31.0 1.0 CD1 A:LEU731 3.9 18.6 1.0 CD1 A:PHE671 4.0 42.7 1.0 C13 A:DXH1001 4.0 32.1 1.0 CZ A:TYR736 4.1 29.3 1.0 OH A:TYR736 4.1 22.2 1.0 CD2 A:HIS738 4.2 22.4 1.0 CD2 A:TYR736 4.2 21.3 1.0 CZ A:PHE671 4.2 36.8 1.0 CD2 A:LEU731 4.3 22.2 1.0 O A:HOH1133 4.4 28.3 1.0 NE2 A:HIS738 4.7 20.3 1.0 C11 A:DXH1001 4.7 32.4 1.0 CG A:LEU731 4.7 21.0 1.0 C12 A:DXH1001 4.9 33.1 1.0 CG2 A:ILE676 4.9 28.1 1.0 CG1 A:VAL756 5.0 19.8 1.0 CB A:ASP758 5.0 28.4 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Ephrin B4 (EPHB4) Receptor Protein Kinase with Nvp-BHG712


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 Ephrin B4 (EPHB4) Receptor Protein Kinase with Nvp-BHG712 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1001 b:29.8 occ:1.00 F19 A:DXH1001 0.0 29.8 1.0 C17 A:DXH1001 1.4 32.0 1.0 F20 A:DXH1001 2.2 29.6 1.0 F18 A:DXH1001 2.2 30.4 1.0 C15 A:DXH1001 2.4 35.8 1.0 C16 A:DXH1001 2.9 31.0 1.0 CG2 A:ILE676 3.5 28.1 1.0 C14 A:DXH1001 3.5 34.8 1.0 O A:VAL756 3.6 21.6 1.0 CD1 A:PHE671 3.8 42.7 1.0 CE1 A:PHE671 4.0 38.7 1.0 CG2 A:ILE677 4.0 34.3 1.0 C11 A:DXH1001 4.1 32.4 1.0 CA A:SER757 4.2 22.4 1.0 C A:VAL756 4.3 24.3 1.0 C A:SER757 4.5 27.2 1.0 N A:SER757 4.6 19.1 1.0 C13 A:DXH1001 4.6 32.1 1.0 O09 A:DXH1001 4.8 35.6 1.0 N A:ILE677 4.8 30.2 1.0 N A:ASP758 4.8 28.8 1.0 CB A:ILE676 4.9 27.6 1.0 CG A:PHE671 4.9 42.5 1.0 C12 A:DXH1001 4.9 33.1 1.0 CG1 A:VAL756 5.0 19.8 1.0 O A:SER757 5.0 24.7 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Ephrin B4 (EPHB4) Receptor Protein Kinase with Nvp-BHG712


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 Ephrin B4 (EPHB4) Receptor Protein Kinase with Nvp-BHG712 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1001 b:29.6 occ:1.00 F20 A:DXH1001 0.0 29.6 1.0 C17 A:DXH1001 1.3 32.0 1.0 F19 A:DXH1001 2.2 29.8 1.0 F18 A:DXH1001 2.2 30.4 1.0 C15 A:DXH1001 2.3 35.8 1.0 C A:SER757 2.9 27.2 1.0 C16 A:DXH1001 3.0 31.0 1.0 O A:SER757 3.0 24.7 1.0 CA A:SER757 3.3 22.4 1.0 C14 A:DXH1001 3.3 34.8 1.0 N A:ASP758 3.4 28.8 1.0 NE2 A:HIS738 3.5 20.3 1.0 N A:SER757 3.6 19.1 1.0 CD2 A:HIS738 3.6 22.4 1.0 O A:VAL756 3.7 21.6 1.0 CB A:ASP758 3.7 28.4 1.0 C A:VAL756 3.8 24.3 1.0 CG1 A:VAL756 3.8 19.8 1.0 CA A:ASP758 4.1 30.9 1.0 C11 A:DXH1001 4.2 32.4 1.0 C13 A:DXH1001 4.5 32.1 1.0 O09 A:DXH1001 4.7 35.6 1.0 CE1 A:HIS738 4.7 22.0 1.0 CB A:SER757 4.7 27.6 1.0 CB A:VAL756 4.7 21.1 1.0 O A:HOH1133 4.8 28.3 1.0 CD1 A:LEU731 4.9 18.6 1.0 C12 A:DXH1001 4.9 33.1 1.0 CG A:HIS738 4.9 21.3 1.0 CA A:VAL756 4.9 23.1 1.0

A.Troster, S.Heinzlmeir, B.T.Berger, S.L.Gande, K.Saxena, S.Sreeramulu, V.Linhard, A.H.Nasiri, M.Bolte, S.Muller, B.Kuster, G.Medard, D.Kudlinzki, H.Schwalbe. Nvp-BHG712: Effects of Regioisomers on the Affinity and Selectivity Toward the Ephrin Family. Chemmedchem V. 13 1629 2018.
ISSN: ESSN 1860-7187
PubMed: 29928781
DOI: 10.1002/CMDC.201800398