Fluorine in PDB 7a5n: Structure of DYRK1A in Complex with Compound 34

All present enzymatic activity of Structure of DYRK1A in Complex with Compound 34:
2.7.12.1;

The structure of Structure of DYRK1A in Complex with Compound 34, PDB code: 7a5n was solved by P.Dokurno, A.E.Surgenor, R.E.Hubbard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.361, 85.368, 84.804, 90, 107.06, 90
R / Rfree (%)	21.9 / 28.5

The structure of Structure of DYRK1A in Complex with Compound 34 also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Fluorine atom in the Structure of DYRK1A in Complex with Compound 34 (pdb code 7a5n). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Structure of DYRK1A in Complex with Compound 34, PDB code: 7a5n:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Structure of DYRK1A in Complex with Compound 34


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of DYRK1A in Complex with Compound 34 within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:39.4 occ:1.00 F1 A:R05501 0.0 39.4 1.0 C15 A:R05501 1.4 39.2 1.0 C14 A:R05501 2.3 37.6 1.0 C16 A:R05501 2.4 36.2 1.0 C13 A:R05501 2.8 35.6 1.0 N5 A:R05501 3.1 36.3 1.0 CG2 A:VAL306 3.4 40.7 1.0 C11 A:R05501 3.5 35.3 1.0 C19 A:R05501 3.6 36.3 1.0 C17 A:R05501 3.6 36.7 1.0 C10 A:R05501 3.6 32.7 1.0 C18 A:R05501 4.1 37.9 1.0 C12 A:R05501 4.2 34.1 1.0 C7 A:R05501 4.3 33.9 1.0 OD1 A:ASN292 4.3 32.1 1.0 N4 A:R05501 4.4 34.0 1.0 CB A:VAL306 4.5 40.3 1.0 O A:GLU291 4.6 32.6 1.0 F2 A:R05501 4.7 40.6 1.0 CD1 A:LEU294 4.8 33.9 1.0 C4 A:R05501 4.8 32.3 1.0 CD2 A:LEU294 4.8 31.2 1.0 C5 A:R05501 4.9 31.2 1.0 C8 A:R05501 5.0 31.5 1.0

Fluorine binding site 2 out of 4 in the Structure of DYRK1A in Complex with Compound 34


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of DYRK1A in Complex with Compound 34 within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:40.6 occ:1.00 F2 A:R05501 0.0 40.6 1.0 C19 A:R05501 1.4 36.3 1.0 C14 A:R05501 2.3 37.6 1.0 C18 A:R05501 2.3 37.9 1.0 C13 A:R05501 2.8 35.6 1.0 N A:GLY166 3.3 42.0 1.0 CA A:GLY166 3.4 40.9 1.0 O A:GLY166 3.5 42.0 1.0 C15 A:R05501 3.6 39.2 1.0 C17 A:R05501 3.6 36.7 1.0 C A:ILE165 3.6 43.1 1.0 N5 A:R05501 3.7 36.3 1.0 CB A:ILE165 3.7 43.8 1.0 C A:GLY166 3.8 42.9 1.0 CB A:VAL173 3.9 48.3 1.0 O A:ILE165 4.0 46.7 1.0 CG1 A:VAL173 4.1 48.7 1.0 C16 A:R05501 4.1 36.2 1.0 CG2 A:ILE165 4.1 47.4 1.0 CA A:ILE165 4.3 44.4 1.0 CG2 A:VAL173 4.3 49.5 1.0 N6 A:R05501 4.6 32.0 1.0 C12 A:R05501 4.6 34.1 1.0 F1 A:R05501 4.7 39.4 1.0 CG1 A:ILE165 4.7 41.5 1.0 N A:LYS167 5.0 46.6 1.0

Fluorine binding site 3 out of 4 in the Structure of DYRK1A in Complex with Compound 34


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of DYRK1A in Complex with Compound 34 within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:70.5 occ:1.00 F1 B:R05501 0.0 70.5 1.0 C15 B:R05501 1.4 69.6 1.0 C16 B:R05501 2.3 66.4 1.0 C14 B:R05501 2.4 67.5 1.0 C13 B:R05501 2.8 64.0 1.0 CG2 B:VAL306 3.3 33.0 1.0 N5 B:R05501 3.6 60.3 1.0 C17 B:R05501 3.6 70.6 1.0 C19 B:R05501 3.6 75.5 1.0 OD1 B:ASN292 3.9 37.2 1.0 C11 B:R05501 4.0 51.9 1.0 C10 B:R05501 4.1 47.8 1.0 C18 B:R05501 4.1 76.9 1.0 O B:GLU291 4.1 36.4 1.0 CB B:VAL306 4.5 32.7 1.0 C12 B:R05501 4.5 55.8 1.0 C7 B:R05501 4.6 49.1 1.0 N4 B:R05501 4.7 41.0 1.0 F2 B:R05501 4.7 70.1 1.0 CB B:ASP307 4.8 33.1 1.0 CD2 B:LEU294 4.9 32.0 1.0 CA B:ASN292 5.0 31.2 1.0

Fluorine binding site 4 out of 4 in the Structure of DYRK1A in Complex with Compound 34


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of DYRK1A in Complex with Compound 34 within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:70.1 occ:1.00 F2 B:R05501 0.0 70.1 1.0 C19 B:R05501 1.4 75.5 1.0 C18 B:R05501 2.3 76.9 1.0 C14 B:R05501 2.4 67.5 1.0 C13 B:R05501 2.9 64.0 1.0 N5 B:R05501 3.4 60.3 1.0 CG2 B:VAL173 3.4 43.1 1.0 CG2 B:ILE165 3.6 52.4 1.0 CA B:GLY166 3.6 60.5 1.0 N B:GLY166 3.6 59.7 1.0 C17 B:R05501 3.6 70.6 1.0 C15 B:R05501 3.6 69.6 1.0 O B:GLY166 3.8 63.0 1.0 CB B:VAL173 3.8 43.5 1.0 C B:ILE165 4.0 54.5 1.0 C B:GLY166 4.1 64.0 1.0 C16 B:R05501 4.1 66.4 1.0 CB B:ILE165 4.2 50.9 1.0 O B:ILE165 4.3 55.3 1.0 C12 B:R05501 4.4 55.8 1.0 CG1 B:VAL173 4.6 47.5 1.0 N6 B:R05501 4.6 54.7 1.0 F1 B:R05501 4.7 70.5 1.0 CA B:ILE165 4.8 49.0 1.0

D.Lee Walmsley, J.B.Murray, P.Dokurno, A.J.Massey, K.Benwell, A.Fiumana, N.Foloppe, S.Ray, J.Smith, A.E.Surgenor, T.Edmonds, D.Demarles, M.Burbridge, F.Cruzalegui, A.Kotschy, R.E.Hubbard. Fragment-Derived Selective Inhibitors of Dual-Specificity Kinases DYRK1A and DYRK1B. J.Med.Chem. 2021.
ISSN: ISSN 0022-2623
PubMed: 34143631
DOI: 10.1021/ACS.JMEDCHEM.1C00024