Fluorine in PDB 8k79: Crystal Structure of C-Src Kinase Domain Bound By Tpx-0022

All present enzymatic activity of Crystal Structure of C-Src Kinase Domain Bound By Tpx-0022:
2.7.10.2;

The structure of Crystal Structure of C-Src Kinase Domain Bound By Tpx-0022, PDB code: 8k79 was solved by L.Z.Qu, Y.H.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 2.80
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	41.863, 63.056, 73.084, 100.48, 91.1, 90.22
R / Rfree (%)	24.1 / 27.7

The binding sites of Fluorine atom in the Crystal Structure of C-Src Kinase Domain Bound By Tpx-0022 (pdb code 8k79). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of C-Src Kinase Domain Bound By Tpx-0022, PDB code: 8k79:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of C-Src Kinase Domain Bound By Tpx-0022


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 C-Src Kinase Domain Bound By Tpx-0022 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:15.3 occ:1.00 F1 A:IYC601 0.0 15.3 1.0 C6 A:IYC601 1.3 16.8 1.0 C5 A:IYC601 2.4 18.4 1.0 C1 A:IYC601 2.4 24.0 1.0 C7 A:IYC601 2.8 37.8 1.0 O A:ASN391 2.9 11.9 1.0 CA A:ASN391 3.2 13.5 1.0 C A:ASN391 3.3 11.5 1.0 CB A:ALA403 3.3 16.8 1.0 N1 A:IYC601 3.6 38.7 1.0 C2 A:IYC601 3.6 27.4 1.0 C4 A:IYC601 3.6 17.8 1.0 N A:ASP404 3.7 31.1 1.0 CB A:ASP404 3.7 25.6 1.0 CB A:ASN391 3.9 10.2 1.0 C A:ALA403 3.9 25.1 1.0 CD1 A:LEU393 4.0 17.1 1.0 O A:ALA390 4.0 12.4 1.0 CG A:LEU393 4.0 13.0 1.0 C3 A:IYC601 4.1 23.5 1.0 OD1 A:ASN391 4.1 10.1 1.0 CA A:ALA403 4.1 24.1 1.0 CA A:ASP404 4.2 25.1 1.0 N A:ILE392 4.4 11.3 1.0 N A:ASN391 4.4 17.3 1.0 CG A:ASN391 4.4 9.7 1.0 O A:ALA403 4.5 21.4 1.0 C A:ALA390 4.7 11.4 1.0 N A:ALA403 4.7 21.4 1.0 CD2 A:LEU393 4.7 13.9 1.0 C8 A:IYC601 4.9 29.1 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of C-Src Kinase Domain Bound By Tpx-0022


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 C-Src Kinase Domain Bound By Tpx-0022 within 5.0Å range: probe atom residue distance (Å) B Occ B:F601 b:29.1 occ:1.00 F1 B:IYC601 0.0 29.1 1.0 C6 B:IYC601 1.4 32.4 1.0 C5 B:IYC601 2.4 23.2 1.0 C1 B:IYC601 2.4 34.2 1.0 C7 B:IYC601 2.8 39.5 1.0 CB B:ALA403 3.3 18.9 1.0 CA B:ASN391 3.5 10.9 1.0 CB B:ASP404 3.6 31.5 1.0 N B:ASP404 3.6 45.0 1.0 N1 B:IYC601 3.6 46.2 1.0 O B:ASN391 3.6 12.8 1.0 C B:ASN391 3.6 10.4 1.0 C4 B:IYC601 3.6 22.1 1.0 C2 B:IYC601 3.6 29.2 1.0 C B:ALA403 3.8 29.4 1.0 O B:ALA390 4.0 15.5 1.0 CA B:ASP404 4.1 33.5 1.0 C3 B:IYC601 4.1 24.9 1.0 CA B:ALA403 4.1 20.7 1.0 OD1 B:ASN391 4.2 15.6 1.0 CB B:ASN391 4.2 13.8 1.0 CG B:LEU393 4.2 14.1 1.0 CD2 B:LEU393 4.4 14.6 1.0 N B:ILE392 4.4 12.9 1.0 O B:ALA403 4.5 28.6 1.0 CG B:ASN391 4.5 17.0 1.0 CD1 B:LEU393 4.5 18.5 1.0 CG B:ASP404 4.6 51.9 1.0 N B:ASN391 4.6 21.5 1.0 C B:ALA390 4.7 10.7 1.0 N B:ALA403 4.7 16.5 1.0 OD1 B:ASP404 4.8 62.1 1.0 C8 B:IYC601 4.9 27.6 1.0

L.Qu, H.Lin, S.Dai, M.Guo, X.Chen, L.Jiang, H.Zhang, M.Li, X.Liang, Z.Chen, H.Wei, Y.Chen. Structural Insight Into the Macrocyclic Inhibitor Tpx-0022 of C-Met and C-Src. Comput Struct Biotechnol J V. 21 5712 2023.
ISSN: ESSN 2001-0370
PubMed: 38074469
DOI: 10.1016/J.CSBJ.2023.11.028