Fluorine in PDB 4u0i: Crystal Structure of Kit in Complex with Ponatinib

All present enzymatic activity of Crystal Structure of Kit in Complex with Ponatinib:
2.7.10.1;

The structure of Crystal Structure of Kit in Complex with Ponatinib, PDB code: 4u0i was solved by T.Zhou, X.Zhu, D.C.Dalgarno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.00
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.032, 70.032, 129.212, 90.00, 90.00, 120.00
R / Rfree (%)	20.4 / 23.9

The binding sites of Fluorine atom in the Crystal Structure of Kit in Complex with Ponatinib (pdb code 4u0i). 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 Kit in Complex with Ponatinib, PDB code: 4u0i:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of Kit in Complex with Ponatinib


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 Kit in Complex with Ponatinib within 5.0Å range: probe atom residue distance (Å) B Occ A:F1001 b:23.2 occ:1.00 F1 A:0LI1001 0.0 23.2 1.0 C19 A:0LI1001 1.3 24.3 1.0 F2 A:0LI1001 2.1 23.2 1.0 F3 A:0LI1001 2.2 25.2 1.0 C17 A:0LI1001 2.3 24.3 1.0 C16 A:0LI1001 3.1 26.0 1.0 CD2 A:HIS790 3.3 19.1 1.0 C20 A:0LI1001 3.4 28.5 1.0 C18 A:0LI1001 3.4 22.8 1.0 NE2 A:HIS790 3.6 20.1 1.0 CG2 A:ILE808 3.7 21.7 1.0 O A:CYS809 4.0 17.6 1.0 CD2 A:LEU783 4.0 25.1 1.0 C A:CYS809 4.1 19.7 1.0 CA A:CYS809 4.2 19.4 1.0 C21 A:0LI1001 4.4 31.3 1.0 CG A:HIS790 4.4 19.8 1.0 N3 A:0LI1001 4.4 30.5 1.0 N A:CYS809 4.4 19.5 1.0 C15 A:0LI1001 4.5 24.4 1.0 C A:ILE808 4.6 19.7 1.0 N A:ASP810 4.6 20.7 1.0 O A:ILE808 4.6 19.5 1.0 CB A:ASP810 4.6 24.9 1.0 C13 A:0LI1001 4.6 24.1 1.0 CE1 A:HIS790 4.7 21.0 1.0 CB A:ILE808 4.8 20.4 1.0 CG A:LEU783 5.0 25.9 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Kit in Complex with Ponatinib


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 Kit in Complex with Ponatinib within 5.0Å range: probe atom residue distance (Å) B Occ A:F1001 b:23.2 occ:1.00 F2 A:0LI1001 0.0 23.2 1.0 C19 A:0LI1001 1.3 24.3 1.0 F3 A:0LI1001 2.1 25.2 1.0 F1 A:0LI1001 2.1 23.2 1.0 C17 A:0LI1001 2.4 24.3 1.0 C18 A:0LI1001 2.7 22.8 1.0 O A:ILE808 3.2 19.5 1.0 CG2 A:ILE653 3.6 20.4 1.0 CA A:CYS809 3.6 19.4 1.0 C A:ILE808 3.7 19.7 1.0 C16 A:0LI1001 3.8 26.0 1.0 CG1 A:VAL654 3.9 22.7 1.0 N A:CYS809 4.0 19.5 1.0 CG2 A:ILE808 4.1 21.7 1.0 C A:CYS809 4.2 19.7 1.0 C13 A:0LI1001 4.2 24.1 1.0 O1 A:0LI1001 4.4 20.6 1.0 C20 A:0LI1001 4.5 28.5 1.0 CD2 A:LEU644 4.6 22.3 1.0 O A:CYS809 4.6 17.6 1.0 CB A:ILE808 4.6 20.4 1.0 N A:ASP810 4.6 20.7 1.0 N A:VAL654 4.8 20.6 1.0 CB A:CYS809 4.8 19.2 1.0 CA A:ILE808 4.8 20.4 1.0 CB A:ILE653 4.9 23.4 1.0 C15 A:0LI1001 4.9 24.4 1.0 CD1 A:LEU647 4.9 19.7 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Kit in Complex with Ponatinib


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 Kit in Complex with Ponatinib within 5.0Å range: probe atom residue distance (Å) B Occ A:F1001 b:25.2 occ:1.00 F3 A:0LI1001 0.0 25.2 1.0 C19 A:0LI1001 1.3 24.3 1.0 F2 A:0LI1001 2.1 23.2 1.0 F1 A:0LI1001 2.2 23.2 1.0 C17 A:0LI1001 2.4 24.3 1.0 C16 A:0LI1001 3.1 26.0 1.0 C20 A:0LI1001 3.2 28.5 1.0 CD1 A:LEU647 3.2 19.7 1.0 C18 A:0LI1001 3.5 22.8 1.0 CD1 A:LEU783 4.0 25.4 1.0 CD2 A:LEU783 4.1 25.1 1.0 CG2 A:ILE653 4.1 20.4 1.0 CG A:LEU783 4.4 25.9 1.0 C15 A:0LI1001 4.4 24.4 1.0 CD2 A:LEU644 4.5 22.3 1.0 N3 A:0LI1001 4.6 30.5 1.0 CG A:LEU647 4.7 20.2 1.0 C13 A:0LI1001 4.7 24.1 1.0 SG A:CYS788 5.0 39.9 1.0

A.P.Garner, J.M.Gozgit, R.Anjum, S.Vodala, A.Schrock, T.Zhou, C.Serrano, G.Eilers, M.Zhu, J.Ketzer, S.Wardwell, Y.Ning, Y.Song, A.Kohlmann, F.Wang, T.Clackson, M.C.Heinrich, J.A.Fletcher, S.Bauer, V.M.Rivera. Ponatinib Inhibits Polyclonal Drug-Resistant Kit Oncoproteins and Shows Therapeutic Potential in Heavily Pretreated Gastrointestinal Stromal Tumor (Gist) Patients. Clin.Cancer Res. 2014.
ISSN: ISSN 1078-0432
PubMed: 25239608
DOI: 10.1158/1078-0432.CCR-14-1397