Fluorine in PDB 3heg: P38 in Complex with Sorafenib

All present enzymatic activity of P38 in Complex with Sorafenib:
2.7.11.24;

The structure of P38 in Complex with Sorafenib, PDB code: 3heg was solved by H.V.Namboodiri, M.Karpusas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.492, 74.249, 77.843, 90.00, 90.00, 90.00
R / Rfree (%)	23.6 / 30.9

The structure of P38 in Complex with Sorafenib also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Fluorine atom in the P38 in Complex with Sorafenib (pdb code 3heg). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the P38 in Complex with Sorafenib, PDB code: 3heg:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the P38 in Complex with Sorafenib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of P38 in Complex with Sorafenib within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:24.3 occ:1.00 F8 A:BAX1 0.0 24.3 1.0 C7 A:BAX1 1.3 23.0 1.0 F10 A:BAX1 2.1 21.9 1.0 F9 A:BAX1 2.1 18.8 1.0 C6 A:BAX1 2.3 25.1 1.0 C5 A:BAX1 3.0 23.5 1.0 CL11 A:BAX1 3.1 25.9 1.0 ND1 A:HIS148 3.1 24.6 1.0 CG2 A:ILE166 3.4 20.6 1.0 C1 A:BAX1 3.5 25.2 1.0 CE1 A:HIS148 3.5 21.5 1.0 CD1 A:ILE141 3.6 26.5 1.0 C4 A:BAX1 4.3 23.5 1.0 CG A:HIS148 4.3 24.5 1.0 C A:LEU167 4.4 24.2 1.0 O A:ILE166 4.4 22.2 1.0 CB A:ILE166 4.4 23.1 1.0 CA A:LEU167 4.4 23.9 1.0 O A:LEU167 4.4 24.5 1.0 CG1 A:ILE141 4.4 24.7 1.0 C A:ILE166 4.4 22.8 1.0 N A:LEU167 4.6 22.7 1.0 C2 A:BAX1 4.6 22.8 1.0 CG1 A:VAL83 4.7 25.2 1.0 NE2 A:HIS148 4.8 23.2 1.0 N A:ASP168 4.9 25.7 1.0 CB A:HIS148 4.9 24.9 1.0 C3 A:BAX1 4.9 25.6 1.0

Fluorine binding site 2 out of 3 in the P38 in Complex with Sorafenib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of P38 in Complex with Sorafenib within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:18.8 occ:1.00 F9 A:BAX1 0.0 18.8 1.0 C7 A:BAX1 1.3 23.0 1.0 F10 A:BAX1 2.1 21.9 1.0 F8 A:BAX1 2.1 24.3 1.0 C6 A:BAX1 2.3 25.1 1.0 C1 A:BAX1 2.7 25.2 1.0 O A:ILE166 3.3 22.2 1.0 CG2 A:ILE84 3.3 25.2 1.0 CG1 A:VAL83 3.4 25.2 1.0 C5 A:BAX1 3.7 23.5 1.0 CA A:LEU167 3.8 23.9 1.0 C A:ILE166 3.9 22.8 1.0 C2 A:BAX1 4.1 22.8 1.0 N A:LEU167 4.2 22.7 1.0 CG2 A:ILE166 4.3 20.6 1.0 C A:LEU167 4.3 24.2 1.0 CL11 A:BAX1 4.5 25.9 1.0 N A:ILE84 4.5 26.1 1.0 O15 A:BAX1 4.5 24.6 1.0 CD2 A:LEU74 4.5 30.3 1.0 CD1 A:ILE141 4.5 26.5 1.0 CB A:ILE84 4.6 25.1 1.0 N A:ASP168 4.7 25.7 1.0 CB A:ILE166 4.7 23.1 1.0 CB A:VAL83 4.8 24.6 1.0 CG A:MET78 4.8 22.7 1.0 C4 A:BAX1 4.8 23.5 1.0 CB A:LEU167 4.8 22.0 1.0 O A:ILE84 4.9 27.2 1.0 O A:LEU167 4.9 24.5 1.0 CA A:ILE166 4.9 22.4 1.0 C3 A:BAX1 4.9 25.6 1.0 N12 A:BAX1 5.0 23.2 1.0

Fluorine binding site 3 out of 3 in the P38 in Complex with Sorafenib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of P38 in Complex with Sorafenib within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:21.9 occ:1.00 F10 A:BAX1 0.0 21.9 1.0 C7 A:BAX1 1.3 23.0 1.0 F8 A:BAX1 2.1 24.3 1.0 F9 A:BAX1 2.1 18.8 1.0 C6 A:BAX1 2.3 25.1 1.0 C5 A:BAX1 3.0 23.5 1.0 CL11 A:BAX1 3.1 25.9 1.0 C1 A:BAX1 3.4 25.2 1.0 CD2 A:LEU74 3.6 30.3 1.0 SD A:MET78 3.7 23.1 1.0 CD1 A:ILE141 3.7 26.5 1.0 CG1 A:VAL83 3.8 25.2 1.0 CG1 A:ILE141 3.8 24.7 1.0 CG A:MET78 4.0 22.7 1.0 C4 A:BAX1 4.3 23.5 1.0 CG A:LEU74 4.6 27.5 1.0 C2 A:BAX1 4.6 22.8 1.0 CD1 A:LEU74 4.6 29.5 1.0 CG2 A:ILE141 4.8 22.7 1.0 C3 A:BAX1 4.9 25.6 1.0 CB A:ILE141 5.0 26.5 1.0

H.V.Namboodiri, M.Bukhtiyarova, J.Ramcharan, M.Karpusas, Y.Lee, E.B.Springman. Analysis of Imatinib and Sorafenib Binding to P38ALPHA Compared with C-Abl and B-Raf Provides Structural Insights For Understanding the Selectivity of Inhibitors Targeting the Dfg-Out Form of Protein Kinases. Biochemistry V. 49 3611 2010.
ISSN: ISSN 0006-2960
PubMed: 20337484
DOI: 10.1021/BI100070R