Fluorine in PDB 7yaz: Crystal Structure of Zak in Complex with Compound Yh-186

All present enzymatic activity of Crystal Structure of Zak in Complex with Compound Yh-186:
2.7.11.25;

The structure of Crystal Structure of Zak in Complex with Compound Yh-186, PDB code: 7yaz was solved by L.L.Kong, C.H.Yun, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.27 / 2.54
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	129.976, 48.608, 42.881, 90, 105.78, 90
R / Rfree (%)	18.4 / 25.2

The binding sites of Fluorine atom in the Crystal Structure of Zak in Complex with Compound Yh-186 (pdb code 7yaz). 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 Zak in Complex with Compound Yh-186, PDB code: 7yaz:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Crystal Structure of Zak in Complex with Compound Yh-186


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 Zak in Complex with Compound Yh-186 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:42.3 occ:0.48 F08 A:IGV401 0.0 42.3 0.5 F08 A:IGV401 0.1 42.3 0.5 C07 A:IGV401 1.4 43.7 0.5 C07 A:IGV401 1.4 43.5 0.5 C09 A:IGV401 2.4 43.9 0.5 C06 A:IGV401 2.4 38.3 0.5 C09 A:IGV401 2.4 44.3 0.5 C06 A:IGV401 2.5 38.3 0.5 N10 A:IGV401 2.9 37.6 0.5 N10 A:IGV401 3.0 39.1 0.5 N A:LYS45 3.4 34.4 1.0 CB A:LYS45 3.4 38.0 1.0 C13 A:IGV401 3.5 38.6 0.5 CG1 A:VAL30 3.5 35.5 1.0 C13 A:IGV401 3.6 39.0 0.5 C40 A:IGV401 3.6 43.7 0.5 C A:VAL44 3.6 38.0 1.0 C40 A:IGV401 3.7 43.7 0.5 C05 A:IGV401 3.7 40.2 0.5 N A:VAL44 3.7 37.3 1.0 CB A:ALA43 3.7 20.1 1.0 C A:ALA43 3.8 29.7 1.0 N11 A:IGV401 3.8 42.2 0.5 C05 A:IGV401 3.8 40.3 0.5 N11 A:IGV401 3.8 42.4 0.5 CA A:LYS45 3.9 42.0 1.0 O A:ILE80 3.9 38.2 1.0 CA A:VAL44 3.9 28.4 1.0 O A:ALA43 4.0 27.9 1.0 CE A:LYS45 4.1 47.2 1.0 C04 A:IGV401 4.1 42.9 0.5 C04 A:IGV401 4.2 42.3 0.5 OG1 A:THR82 4.2 24.4 1.0 O A:VAL44 4.3 37.5 1.0 CG2 A:THR82 4.3 24.6 1.0 CA A:ALA43 4.4 28.8 1.0 C14 A:IGV401 4.5 40.5 0.5 CB A:VAL30 4.6 42.8 1.0 C14 A:IGV401 4.6 40.4 0.5 N12 A:IGV401 4.6 43.5 0.5 CG2 A:VAL30 4.6 47.1 1.0 CG A:LYS45 4.7 39.0 1.0 N12 A:IGV401 4.7 42.1 0.5 F41 A:IGV401 4.7 47.6 0.5 F41 A:IGV401 4.8 47.6 0.5 C A:ILE80 4.9 37.5 1.0 CB A:THR82 4.9 24.3 1.0 CD A:LYS45 4.9 40.3 1.0

Fluorine binding site 2 out of 4 in the Crystal Structure of Zak in Complex with Compound Yh-186


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 Zak in Complex with Compound Yh-186 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:42.3 occ:0.52 F08 A:IGV401 0.0 42.3 0.5 F08 A:IGV401 0.1 42.3 0.5 C07 A:IGV401 1.3 43.7 0.5 C07 A:IGV401 1.4 43.5 0.5 C06 A:IGV401 2.3 38.3 0.5 C09 A:IGV401 2.4 43.9 0.5 C06 A:IGV401 2.4 38.3 0.5 C09 A:IGV401 2.4 44.3 0.5 N10 A:IGV401 3.0 37.6 0.5 N10 A:IGV401 3.1 39.1 0.5 N A:LYS45 3.3 34.4 1.0 CB A:LYS45 3.4 38.0 1.0 C05 A:IGV401 3.6 40.2 0.5 C13 A:IGV401 3.6 38.6 0.5 C40 A:IGV401 3.6 43.7 0.5 C40 A:IGV401 3.6 43.7 0.5 CG1 A:VAL30 3.6 35.5 1.0 C13 A:IGV401 3.6 39.0 0.5 C A:VAL44 3.7 38.0 1.0 C05 A:IGV401 3.7 40.3 0.5 N A:VAL44 3.8 37.3 1.0 O A:ILE80 3.8 38.2 1.0 CA A:LYS45 3.8 42.0 1.0 C A:ALA43 3.8 29.7 1.0 N11 A:IGV401 3.8 42.2 0.5 CB A:ALA43 3.9 20.1 1.0 N11 A:IGV401 3.9 42.4 0.5 CA A:VAL44 3.9 28.4 1.0 O A:ALA43 4.0 27.9 1.0 C04 A:IGV401 4.1 42.9 0.5 CE A:LYS45 4.1 47.2 1.0 C04 A:IGV401 4.1 42.3 0.5 OG1 A:THR82 4.2 24.4 1.0 CG2 A:THR82 4.2 24.6 1.0 O A:VAL44 4.3 37.5 1.0 CA A:ALA43 4.5 28.8 1.0 C14 A:IGV401 4.6 40.5 0.5 CG A:LYS45 4.7 39.0 1.0 CG2 A:VAL30 4.7 47.1 1.0 CB A:VAL30 4.7 42.8 1.0 N12 A:IGV401 4.7 43.5 0.5 C14 A:IGV401 4.7 40.4 0.5 F41 A:IGV401 4.7 47.6 0.5 F41 A:IGV401 4.8 47.6 0.5 C A:ILE80 4.8 37.5 1.0 N12 A:IGV401 4.8 42.1 0.5 CB A:THR82 4.9 24.3 1.0 CD A:LYS45 4.9 40.3 1.0 N A:THR82 5.0 30.2 1.0 CG2 A:ILE80 5.0 39.2 1.0

Fluorine binding site 3 out of 4 in the Crystal Structure of Zak in Complex with Compound Yh-186


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 Zak in Complex with Compound Yh-186 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:47.6 occ:0.48 F41 A:IGV401 0.0 47.6 0.5 F41 A:IGV401 0.1 47.6 0.5 C40 A:IGV401 1.4 43.7 0.5 C40 A:IGV401 1.4 43.7 0.5 C09 A:IGV401 2.3 44.3 0.5 C04 A:IGV401 2.3 42.9 0.5 C09 A:IGV401 2.3 43.9 0.5 C04 A:IGV401 2.4 42.3 0.5 N10 A:IGV401 2.5 37.6 0.5 N10 A:IGV401 2.6 39.1 0.5 N03 A:IGV401 2.6 39.6 0.5 N03 A:IGV401 2.7 39.5 0.5 N11 A:IGV401 2.9 42.2 0.5 N11 A:IGV401 2.9 42.4 0.5 CB A:CYS150 2.9 31.0 1.0 N A:ASP151 3.2 38.9 1.0 C13 A:IGV401 3.2 38.6 0.5 C13 A:IGV401 3.3 39.0 0.5 SG A:CYS150 3.4 36.2 1.0 CA A:CYS150 3.4 33.4 1.0 C05 A:IGV401 3.6 40.2 0.5 C07 A:IGV401 3.6 43.7 0.5 C07 A:IGV401 3.6 43.5 0.5 C05 A:IGV401 3.7 40.3 0.5 N12 A:IGV401 3.7 43.5 0.5 N12 A:IGV401 3.8 42.1 0.5 C A:CYS150 3.8 36.0 1.0 C14 A:IGV401 3.9 40.5 0.5 CG2 A:ILE66 3.9 26.1 1.0 C14 A:IGV401 4.0 40.4 0.5 CA A:ASP151 4.1 32.6 1.0 C06 A:IGV401 4.1 38.3 0.5 C06 A:IGV401 4.1 38.3 0.5 S02 A:IGV401 4.3 41.8 0.5 S02 A:IGV401 4.4 41.9 0.5 CB A:ASP151 4.6 32.3 1.0 CB A:ILE66 4.7 24.7 1.0 F08 A:IGV401 4.7 42.3 0.5 F08 A:IGV401 4.7 42.3 0.5 CE A:LYS45 4.8 47.2 1.0 OD1 A:ASP151 4.8 49.7 1.0 N A:CYS150 4.8 31.1 1.0 NZ A:LYS45 4.8 40.2 1.0 O01 A:IGV401 4.9 53.6 0.5 O54 A:IGV401 4.9 45.8 0.5 CG1 A:ILE66 4.9 33.8 1.0 O A:CYS150 5.0 29.5 1.0

Fluorine binding site 4 out of 4 in the Crystal Structure of Zak in Complex with Compound Yh-186


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 Zak in Complex with Compound Yh-186 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:47.6 occ:0.52 F41 A:IGV401 0.0 47.6 0.5 F41 A:IGV401 0.1 47.6 0.5 C40 A:IGV401 1.3 43.7 0.5 C40 A:IGV401 1.4 43.7 0.5 C04 A:IGV401 2.2 42.9 0.5 C04 A:IGV401 2.3 42.3 0.5 C09 A:IGV401 2.4 44.3 0.5 C09 A:IGV401 2.4 43.9 0.5 N03 A:IGV401 2.5 39.6 0.5 N10 A:IGV401 2.6 37.6 0.5 N03 A:IGV401 2.6 39.5 0.5 N10 A:IGV401 2.6 39.1 0.5 N11 A:IGV401 2.9 42.2 0.5 N11 A:IGV401 3.0 42.4 0.5 CB A:CYS150 3.0 31.0 1.0 N A:ASP151 3.1 38.9 1.0 C13 A:IGV401 3.3 38.6 0.5 C13 A:IGV401 3.4 39.0 0.5 CA A:CYS150 3.4 33.4 1.0 SG A:CYS150 3.5 36.2 1.0 C05 A:IGV401 3.5 40.2 0.5 C05 A:IGV401 3.6 40.3 0.5 C07 A:IGV401 3.6 43.7 0.5 C07 A:IGV401 3.6 43.5 0.5 C A:CYS150 3.7 36.0 1.0 N12 A:IGV401 3.8 43.5 0.5 N12 A:IGV401 3.9 42.1 0.5 CA A:ASP151 3.9 32.6 1.0 CG2 A:ILE66 4.0 26.1 1.0 C14 A:IGV401 4.0 40.5 0.5 C06 A:IGV401 4.1 38.3 0.5 C06 A:IGV401 4.1 38.3 0.5 C14 A:IGV401 4.1 40.4 0.5 S02 A:IGV401 4.1 41.8 0.5 S02 A:IGV401 4.3 41.9 0.5 CB A:ASP151 4.5 32.3 1.0 OD1 A:ASP151 4.7 49.7 1.0 CE A:LYS45 4.7 47.2 1.0 O01 A:IGV401 4.7 53.6 0.5 F08 A:IGV401 4.8 42.3 0.5 CB A:ILE66 4.8 24.7 1.0 F08 A:IGV401 4.8 42.3 0.5 O54 A:IGV401 4.8 45.8 0.5 NZ A:LYS45 4.8 40.2 1.0 N A:CYS150 4.8 31.1 1.0 O01 A:IGV401 4.9 53.8 0.5 O54 A:IGV401 4.9 45.8 0.5 O A:CYS150 4.9 29.5 1.0

Y.Zhou, H.Yu, A.C.Vind, L.Kong, Y.Liu, X.Song, Z.Tu, C.Yun, J.B.Smaill, Q.W.Zhang, K.Ding, S.Bekker-Jensen, X.Lu. Rational Design of Covalent Kinase Inhibitors By An Integrated Computational Workflow (Kin-Cov). J.Med.Chem. V. 66 7405 2023.
ISSN: ISSN 0022-2623
PubMed: 37220641
DOI: 10.1021/ACS.JMEDCHEM.3C00088