Fluorine in PDB 7wcl: Crystal Structure of FGFR1 Kinase Domain with Pemigatinib

All present enzymatic activity of Crystal Structure of FGFR1 Kinase Domain with Pemigatinib:
2.7.10.1;

The structure of Crystal Structure of FGFR1 Kinase Domain with Pemigatinib, PDB code: 7wcl was solved by X.J.Chen, Q.M.Lin, L.Y.Jiang, 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)	39.87 / 2.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	210.831, 49.594, 66.804, 90, 107.5, 90
R / Rfree (%)	19.3 / 23

The binding sites of Fluorine atom in the Crystal Structure of FGFR1 Kinase Domain with Pemigatinib (pdb code 7wcl). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of FGFR1 Kinase Domain with Pemigatinib, PDB code: 7wcl:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Crystal Structure of FGFR1 Kinase Domain with Pemigatinib


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 FGFR1 Kinase Domain with Pemigatinib within 5.0Å range: probe atom residue distance (Å) B Occ A:F801 b:35.0 occ:1.00 FAL A:8ZF801 0.0 35.0 1.0 CAE A:8ZF801 1.4 34.0 1.0 CAF A:8ZF801 2.4 33.9 1.0 CAD A:8ZF801 2.4 32.6 1.0 OAG A:8ZF801 2.6 33.3 1.0 NAM A:8ZF801 2.7 33.0 1.0 CB A:ALA640 3.2 33.4 1.0 CAP A:8ZF801 3.2 35.0 1.0 CAN A:8ZF801 3.3 30.8 1.0 OAU A:8ZF801 3.5 30.1 1.0 CAA A:8ZF801 3.7 36.9 1.0 CAC A:8ZF801 3.7 30.7 1.0 CD1 A:LEU630 3.7 30.9 1.0 CAH A:8ZF801 3.8 31.6 1.0 CG1 A:ILE545 3.9 34.1 1.0 CA A:ALA640 4.0 30.6 1.0 CG2 A:ILE545 4.0 31.8 1.0 CAR A:8ZF801 4.0 33.9 1.0 NAO A:8ZF801 4.1 32.3 1.0 CAB A:8ZF801 4.1 32.1 1.0 CB A:ILE545 4.2 30.1 1.0 O A:HOH936 4.3 38.5 1.0 OD1 A:ASP641 4.3 50.0 1.0 O A:HOH928 4.3 40.2 1.0 N A:ASP641 4.3 33.4 1.0 CAQ A:8ZF801 4.4 33.2 1.0 C A:ALA640 4.7 35.8 1.0 CD1 A:ILE545 4.7 30.8 1.0 CG A:LEU630 4.8 38.8 1.0 FAK A:8ZF801 4.9 35.3 1.0 CG A:ASP641 5.0 42.0 1.0 CAV A:8ZF801 5.0 33.7 1.0 CAT A:8ZF801 5.0 30.4 1.0

Fluorine binding site 2 out of 4 in the Crystal Structure of FGFR1 Kinase Domain with Pemigatinib


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 FGFR1 Kinase Domain with Pemigatinib within 5.0Å range: probe atom residue distance (Å) B Occ A:F801 b:35.3 occ:1.00 FAK A:8ZF801 0.0 35.3 1.0 CAC A:8ZF801 1.4 30.7 1.0 CAB A:8ZF801 2.4 32.1 1.0 CAD A:8ZF801 2.4 32.6 1.0 OAI A:8ZF801 2.7 31.8 1.0 NAM A:8ZF801 2.9 33.0 1.0 CB A:LYS514 3.2 35.3 1.0 CG2 A:VAL561 3.5 30.6 1.0 CG2 A:VAL492 3.5 31.6 1.0 CAN A:8ZF801 3.5 30.8 1.0 CAP A:8ZF801 3.6 35.0 1.0 CG1 A:VAL492 3.6 32.1 1.0 CAE A:8ZF801 3.7 34.0 1.0 CAA A:8ZF801 3.7 36.9 1.0 OAU A:8ZF801 3.7 30.1 1.0 CD A:LYS514 3.9 36.6 1.0 CG A:LYS514 3.9 33.5 1.0 O A:HOH928 3.9 40.2 1.0 N A:LYS514 4.0 37.0 1.0 CA A:LYS514 4.0 37.5 1.0 CAJ A:8ZF801 4.1 29.8 1.0 CAF A:8ZF801 4.2 33.9 1.0 CB A:VAL492 4.2 37.2 1.0 C A:VAL513 4.5 36.2 1.0 NAO A:8ZF801 4.6 32.3 1.0 CAR A:8ZF801 4.6 33.9 1.0 CB A:ALA512 4.7 32.1 1.0 CB A:VAL561 4.7 31.2 1.0 CG1 A:VAL561 4.7 26.9 1.0 O A:VAL559 4.8 26.5 1.0 FAL A:8ZF801 4.9 35.0 1.0 O A:ALA512 4.9 27.9 1.0 O A:VAL513 4.9 35.9 1.0 C A:ALA512 5.0 27.5 1.0

Fluorine binding site 3 out of 4 in the Crystal Structure of FGFR1 Kinase Domain with Pemigatinib


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 FGFR1 Kinase Domain with Pemigatinib within 5.0Å range: probe atom residue distance (Å) B Occ B:F801 b:43.0 occ:1.00 FAL B:8ZF801 0.0 43.0 1.0 CAE B:8ZF801 1.3 45.7 1.0 CAD B:8ZF801 2.4 48.7 1.0 CAF B:8ZF801 2.4 44.4 1.0 NAM B:8ZF801 2.6 51.0 1.0 OAG B:8ZF801 2.7 41.7 1.0 CB B:ALA640 3.2 39.5 1.0 CAP B:8ZF801 3.2 50.2 1.0 CAN B:8ZF801 3.3 44.7 1.0 OAU B:8ZF801 3.4 49.0 1.0 CAC B:8ZF801 3.6 43.7 1.0 CAA B:8ZF801 3.6 42.6 1.0 CG1 B:ILE545 3.8 37.0 1.0 CD1 B:LEU630 3.9 48.0 1.0 CG2 B:ILE545 3.9 37.2 1.0 CA B:ALA640 4.0 38.7 1.0 CAH B:8ZF801 4.0 38.8 1.0 CAR B:8ZF801 4.1 46.2 1.0 OD1 B:ASP641 4.1 51.6 1.0 NAO B:8ZF801 4.1 49.4 1.0 CAB B:8ZF801 4.1 42.1 1.0 CB B:ILE545 4.1 39.9 1.0 N B:ASP641 4.1 39.0 1.0 CAQ B:8ZF801 4.5 48.4 1.0 O B:HOH928 4.5 61.6 1.0 C B:ALA640 4.6 42.5 1.0 CD1 B:ILE545 4.7 32.4 1.0 FAK B:8ZF801 4.7 46.2 1.0 CG B:ASP641 4.9 43.6 1.0 CG B:LEU630 4.9 35.6 1.0

Fluorine binding site 4 out of 4 in the Crystal Structure of FGFR1 Kinase Domain with Pemigatinib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of FGFR1 Kinase Domain with Pemigatinib within 5.0Å range: probe atom residue distance (Å) B Occ B:F801 b:46.2 occ:1.00 FAK B:8ZF801 0.0 46.2 1.0 CAC B:8ZF801 1.3 43.7 1.0 CAD B:8ZF801 2.4 48.7 1.0 CAB B:8ZF801 2.4 42.1 1.0 OAI B:8ZF801 2.7 42.2 1.0 NAM B:8ZF801 2.8 51.0 1.0 CG2 B:VAL492 3.4 43.3 1.0 CB B:LYS514 3.5 37.0 1.0 CAN B:8ZF801 3.5 44.7 1.0 CAP B:8ZF801 3.5 50.2 1.0 CG2 B:VAL561 3.5 34.0 1.0 CG1 B:VAL492 3.6 38.9 1.0 CAE B:8ZF801 3.6 45.7 1.0 CD B:LYS514 3.7 45.6 1.0 CAA B:8ZF801 3.7 42.6 1.0 OAU B:8ZF801 3.7 49.0 1.0 CG B:LYS514 4.1 38.5 1.0 CAJ B:8ZF801 4.1 44.6 1.0 CAF B:8ZF801 4.1 44.4 1.0 CB B:VAL492 4.1 40.5 1.0 CA B:LYS514 4.4 43.3 1.0 N B:LYS514 4.4 39.7 1.0 NAO B:8ZF801 4.5 49.4 1.0 CAR B:8ZF801 4.5 46.2 1.0 CB B:ALA512 4.7 34.3 1.0 C B:VAL513 4.7 37.8 1.0 FAL B:8ZF801 4.7 43.0 1.0 CB B:VAL561 4.8 35.5 1.0 CG1 B:VAL561 4.9 34.1 1.0 CE B:LYS514 4.9 46.8 1.0 O B:VAL513 5.0 35.9 1.0

Q.Lin, X.Chen, L.Qu, M.Guo, H.Wei, S.Dai, L.Jiang, Y.Chen. Characterization of the Cholangiocarcinoma Drug Pemigatinib Against Fgfr Gatekeeper Mutants Commun Chem V. 5 2022.
ISSN: ESSN 2399-3669
DOI: 10.1038/S42004-022-00718-Z