Fluorine in PDB 9gla: Crystal Structure of A CDK2-Based CDK7 Mimic with Inhibitor SY5609

All present enzymatic activity of Crystal Structure of A CDK2-Based CDK7 Mimic with Inhibitor SY5609:
2.7.11.22;

The structure of Crystal Structure of A CDK2-Based CDK7 Mimic with Inhibitor SY5609, PDB code: 9gla was solved by J.Skerlova, V.Krejcirikova, P.Rezacova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.46 / 2.18
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	71.937, 109.786, 163.554, 90, 90, 90
R / Rfree (%)	20.1 / 24.9

The structure of Crystal Structure of A CDK2-Based CDK7 Mimic with Inhibitor SY5609 also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Fluorine atom in the Crystal Structure of A CDK2-Based CDK7 Mimic with Inhibitor SY5609 (pdb code 9gla). 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 A CDK2-Based CDK7 Mimic with Inhibitor SY5609, PDB code: 9gla:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of A CDK2-Based CDK7 Mimic with Inhibitor SY5609


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 A CDK2-Based CDK7 Mimic with Inhibitor SY5609 within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:47.4 occ:1.00 F32 A:YNK301 0.0 47.4 1.0 C31 A:YNK301 1.4 45.9 1.0 F33 A:YNK301 2.2 44.7 1.0 F34 A:YNK301 2.2 47.5 1.0 C13 A:YNK301 2.4 42.0 1.0 C17 A:YNK301 2.9 49.5 1.0 C14 A:YNK301 3.0 42.2 1.0 C16 A:YNK301 3.0 43.8 1.0 C12 A:YNK301 3.6 43.4 1.0 CD2 A:PHE80 3.8 37.5 1.0 N18 A:YNK301 3.9 47.7 1.0 O A:HOH415 4.0 55.7 1.0 CB A:ALA31 4.0 41.2 1.0 CG A:PHE80 4.1 33.2 1.0 C26 A:YNK301 4.1 48.0 1.0 N15 A:YNK301 4.2 39.4 1.0 CE A:LYS33 4.2 66.5 1.0 CB A:PHE80 4.3 37.9 1.0 CE2 A:PHE80 4.3 37.5 1.0 OD1 A:ASP145 4.5 53.6 1.0 C19 A:YNK301 4.5 50.0 1.0 CG1 A:VAL18 4.6 40.2 1.0 N11 A:YNK301 4.7 42.9 1.0 NZ A:LYS33 4.7 65.2 1.0 CD1 A:PHE80 4.8 35.2 1.0 C10 A:YNK301 4.9 42.5 1.0 CG2 A:VAL18 5.0 40.6 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of A CDK2-Based CDK7 Mimic with Inhibitor SY5609


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 A CDK2-Based CDK7 Mimic with Inhibitor SY5609 within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:44.7 occ:1.00 F33 A:YNK301 0.0 44.7 1.0 C31 A:YNK301 1.4 45.9 1.0 F34 A:YNK301 2.2 47.5 1.0 F32 A:YNK301 2.2 47.4 1.0 C13 A:YNK301 2.4 42.0 1.0 C17 A:YNK301 3.0 49.5 1.0 O A:HOH415 3.1 55.7 1.0 C14 A:YNK301 3.2 42.2 1.0 C12 A:YNK301 3.4 43.4 1.0 C16 A:YNK301 3.5 43.8 1.0 CD1 A:LEU134 3.5 46.3 1.0 CB A:ALA144 3.8 34.8 1.0 CG1 A:ILE64 3.9 41.6 1.0 OD1 A:ASP145 4.1 53.6 1.0 CD1 A:ILE64 4.1 43.9 1.0 N18 A:YNK301 4.2 47.7 1.0 N15 A:YNK301 4.4 39.4 1.0 CG A:PHE80 4.4 33.2 1.0 N11 A:YNK301 4.6 42.9 1.0 CB A:PHE80 4.6 37.9 1.0 CD1 A:PHE80 4.6 35.2 1.0 CD2 A:PHE80 4.7 37.5 1.0 CG A:LEU134 4.8 44.1 1.0 C26 A:YNK301 4.8 48.0 1.0 CB A:ILE64 4.8 38.8 1.0 CG A:ASP145 4.9 56.4 1.0 C10 A:YNK301 4.9 42.5 1.0 N A:ASP145 5.0 41.2 1.0 CA A:ALA144 5.0 36.9 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of A CDK2-Based CDK7 Mimic with Inhibitor SY5609


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 A CDK2-Based CDK7 Mimic with Inhibitor SY5609 within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:47.5 occ:1.00 F34 A:YNK301 0.0 47.5 1.0 C31 A:YNK301 1.3 45.9 1.0 F33 A:YNK301 2.2 44.7 1.0 F32 A:YNK301 2.2 47.4 1.0 C13 A:YNK301 2.3 42.0 1.0 C12 A:YNK301 2.6 43.4 1.0 CB A:PHE80 2.9 37.9 1.0 CG A:PHE80 3.3 33.2 1.0 O A:GLU81 3.5 40.4 1.0 C14 A:YNK301 3.6 42.2 1.0 CB A:ALA31 3.6 41.2 1.0 CD2 A:PHE80 3.8 37.5 1.0 CG1 A:ILE64 3.9 41.6 1.0 CD1 A:ILE64 3.9 43.9 1.0 N11 A:YNK301 4.0 42.9 1.0 CD1 A:PHE80 4.0 35.2 1.0 CA A:PHE80 4.3 35.4 1.0 C16 A:YNK301 4.4 43.8 1.0 C17 A:YNK301 4.5 49.5 1.0 CD1 A:LEU134 4.5 46.3 1.0 C A:PHE80 4.5 34.9 1.0 O A:HOH415 4.6 55.7 1.0 C A:GLU81 4.6 39.4 1.0 N15 A:YNK301 4.6 39.4 1.0 C10 A:YNK301 4.7 42.5 1.0 CE2 A:PHE80 4.7 37.5 1.0 N A:GLU81 4.9 36.2 1.0 O A:ALA31 4.9 45.5 1.0 O A:PHE80 4.9 36.0 1.0 CE1 A:PHE80 4.9 36.2 1.0 CA A:ALA31 4.9 41.3 1.0

J.Skerlova, V.Krejcirikova, M.Perina, V.Vojackova, M.Fabry, V.Krystof, R.Jorda, P.Rezacova. CDK2-Based CDK7 Mimic As A Tool For Structural Analysis: Biochemical Validation and Crystal Structure with SY5609. Int.J.Biol.Macromol. V. 294 39117 2025.
ISSN: ISSN 0141-8130
PubMed: 39733900
DOI: 10.1016/J.IJBIOMAC.2024.139117