Chlorine in PDB 8f7o: Braf Kinase in Complex with TAK580 (Tovorafenib)

All present enzymatic activity of Braf Kinase in Complex with TAK580 (Tovorafenib):
2.7.11.1;

The structure of Braf Kinase in Complex with TAK580 (Tovorafenib), PDB code: 8f7o was solved by E.Tkacik, K.Li, G.Gonzalez Del-Pino, M.J.Eck, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	70.79 / 3.54
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	86.918, 121.998, 57.797, 90, 90, 90
R / Rfree (%)	21.5 / 26.9

The structure of Braf Kinase in Complex with TAK580 (Tovorafenib) also contains other interesting chemical elements:

Fluorine

(F)

6 atoms

The binding sites of Chlorine atom in the Braf Kinase in Complex with TAK580 (Tovorafenib) (pdb code 8f7o). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Braf Kinase in Complex with TAK580 (Tovorafenib), PDB code: 8f7o:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Braf Kinase in Complex with TAK580 (Tovorafenib)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Braf Kinase in Complex with TAK580 (Tovorafenib) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl801 b:108.3 occ:1.00 CL20 A:QOP801 0.0 108.3 1.0 C19 A:QOP801 1.8 97.8 1.0 C18 A:QOP801 2.8 103.3 1.0 C21 A:QOP801 2.8 94.9 1.0 F24 A:QOP801 2.9 94.7 1.0 C22 A:QOP801 3.1 96.3 1.0 F23 A:QOP801 3.2 106.4 1.0 CA A:HIS574 3.8 79.3 1.0 N17 A:QOP801 4.0 98.8 1.0 O A:ILE573 4.0 86.7 1.0 C26 A:QOP801 4.0 92.4 1.0 O A:HIS574 4.1 87.1 1.0 CG A:HIS574 4.2 81.4 1.0 CD2 A:HIS574 4.2 88.4 1.0 CG2 A:ILE572 4.3 79.2 1.0 CG1 A:VAL504 4.4 71.7 1.0 C A:HIS574 4.4 93.2 1.0 CB A:HIS574 4.5 77.5 1.0 F25 A:QOP801 4.5 90.3 1.0 C16 A:QOP801 4.5 90.8 1.0 N A:HIS574 4.6 64.1 1.0 C A:ILE573 4.6 80.1 1.0 ND1 A:HIS574 4.6 84.8 1.0 NE2 A:HIS574 4.6 87.8 1.0 CE1 A:HIS574 4.9 83.5 1.0

Chlorine binding site 2 out of 4 in the Braf Kinase in Complex with TAK580 (Tovorafenib)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Braf Kinase in Complex with TAK580 (Tovorafenib) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl801 b:115.3 occ:1.00 CL32 A:QOP801 0.0 115.3 1.0 C31 A:QOP801 1.8 82.4 1.0 C02 A:QOP801 2.8 86.7 1.0 C06 A:QOP801 2.8 82.9 1.0 O30 A:QOP801 2.8 81.2 1.0 N01 A:QOP801 3.0 81.0 1.0 C07 A:QOP801 3.2 80.6 1.0 N03 A:QOP801 4.0 89.2 1.0 N05 A:QOP801 4.0 85.1 1.0 O A:ALA598 4.1 107.0 1.0 CA A:ALA598 4.2 102.3 1.0 O A:LEU597 4.2 99.3 1.0 CZ3 A:TRP531 4.2 85.0 1.0 CG1 A:VAL471 4.2 81.5 1.0 C04 A:QOP801 4.5 84.7 1.0 CG2 A:ILE463 4.5 139.3 1.0 N08 A:QOP801 4.6 80.3 1.0 C A:ALA598 4.6 111.0 1.0 CB A:ALA598 4.8 85.2 1.0 CH2 A:TRP531 4.8 99.1 1.0 CE3 A:TRP531 5.0 81.0 1.0 CB A:ILE463 5.0 133.1 1.0

Chlorine binding site 3 out of 4 in the Braf Kinase in Complex with TAK580 (Tovorafenib)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Braf Kinase in Complex with TAK580 (Tovorafenib) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl801 b:115.0 occ:1.00 CL20 B:QOP801 0.0 115.0 1.0 C19 B:QOP801 1.8 105.0 1.0 C18 B:QOP801 2.8 107.6 1.0 C21 B:QOP801 2.8 100.1 1.0 F24 B:QOP801 2.9 111.6 1.0 C22 B:QOP801 3.1 107.2 1.0 F23 B:QOP801 3.1 112.1 1.0 CG1 B:VAL504 4.0 95.8 1.0 N17 B:QOP801 4.0 103.7 1.0 C26 B:QOP801 4.0 95.2 1.0 O B:ILE573 4.4 92.2 1.0 CA B:HIS574 4.4 90.8 1.0 F25 B:QOP801 4.4 109.0 1.0 O B:HIS574 4.5 103.4 1.0 CG2 B:ILE572 4.5 75.4 1.0 C16 B:QOP801 4.5 96.6 1.0 CB B:ASP594 4.8 118.1 1.0 CD2 B:HIS574 4.8 93.1 1.0 CG B:HIS574 4.8 93.0 1.0 OD2 B:ASP594 4.8 120.3 1.0 C B:HIS574 4.9 98.3 1.0 CB B:VAL504 5.0 89.7 1.0

Chlorine binding site 4 out of 4 in the Braf Kinase in Complex with TAK580 (Tovorafenib)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Braf Kinase in Complex with TAK580 (Tovorafenib) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl801 b:119.0 occ:1.00 CL32 B:QOP801 0.0 119.0 1.0 C31 B:QOP801 1.8 82.0 1.0 C02 B:QOP801 2.7 87.9 1.0 C06 B:QOP801 2.8 84.7 1.0 O30 B:QOP801 2.9 80.8 1.0 N01 B:QOP801 3.0 79.3 1.0 C07 B:QOP801 3.2 76.1 1.0 CG2 B:ILE463 3.8 124.2 1.0 N03 B:QOP801 4.0 102.8 1.0 N05 B:QOP801 4.0 94.1 1.0 CZ3 B:TRP531 4.2 105.7 1.0 C04 B:QOP801 4.5 98.9 1.0 N08 B:QOP801 4.6 75.0 1.0 CB B:ILE463 4.7 121.6 1.0 CH2 B:TRP531 4.7 112.2 1.0 CG1 B:VAL471 4.8 86.9 1.0 CG1 B:ILE463 4.9 101.8 1.0 CE1 B:PHE595 4.9 93.8 1.0 CE3 B:TRP531 4.9 101.0 1.0

E.Tkacik, K.Li, G.Gonzalez-Del Pino, B.H.Ha, J.Vinals, E.Park, T.S.Beyett, M.J.Eck. Structure and Raf-Family Kinase Isoform Selectivity of Type II Raf Inhibitors Tovorafenib and Naporafenib. J.Biol.Chem. 04634 2023.
ISSN: ESSN 1083-351X
PubMed: 36963492
DOI: 10.1016/J.JBC.2023.104634