Fluorine in PDB 6myn: Crystal Structure of Murine Nf-Kappab Inducing Kinase (Nik) Bound to Inhibitor R7

All present enzymatic activity of Crystal Structure of Murine Nf-Kappab Inducing Kinase (Nik) Bound to Inhibitor R7:
2.7.11.25;

The structure of Crystal Structure of Murine Nf-Kappab Inducing Kinase (Nik) Bound to Inhibitor R7, PDB code: 6myn was solved by S.F.Harris, M.Smith, J.Barker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.19 / 2.74
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	143.220, 143.220, 46.410, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 25.5

The binding sites of Fluorine atom in the Crystal Structure of Murine Nf-Kappab Inducing Kinase (Nik) Bound to Inhibitor R7 (pdb code 6myn). 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 Murine Nf-Kappab Inducing Kinase (Nik) Bound to Inhibitor R7, PDB code: 6myn:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of Murine Nf-Kappab Inducing Kinase (Nik) Bound to Inhibitor R7


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 Murine Nf-Kappab Inducing Kinase (Nik) Bound to Inhibitor R7 within 5.0Å range: probe atom residue distance (Å) B Occ A:F703 b:48.0 occ:0.64 F17 A:K6Y703 0.0 48.0 0.6 C16 A:K6Y703 1.3 50.9 0.6 OD2 A:ASP536 1.9 55.7 1.0 C15 A:K6Y703 2.3 49.8 0.6 C11 A:K6Y703 2.4 47.8 0.6 CG A:ASP536 2.9 57.6 1.0 C10 A:K6Y703 2.9 46.1 0.6 CB A:ASP536 3.1 46.7 1.0 CE A:LYS431 3.5 42.3 1.0 C12 A:K6Y703 3.6 48.9 0.6 C14 A:K6Y703 3.6 46.2 0.6 C9 A:K6Y703 3.8 49.0 0.6 CD A:LYS431 3.9 40.1 1.0 CA A:ASP536 4.0 44.7 1.0 OE2 A:GLU415 4.0 51.7 1.0 OD1 A:ASP536 4.0 62.5 1.0 C13 A:K6Y703 4.1 45.8 0.6 NZ A:LYS431 4.1 41.3 1.0 CG A:LYS431 4.3 35.5 1.0 CG2 A:VAL416 4.5 32.4 1.0 OD1 A:ASN522 4.5 53.6 1.0 N A:ASP536 4.6 45.4 1.0 C18 A:K6Y703 4.9 50.0 0.6 C7 A:K6Y703 5.0 54.7 0.6

Fluorine binding site 2 out of 2 in the Crystal Structure of Murine Nf-Kappab Inducing Kinase (Nik) Bound to Inhibitor R7


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 Murine Nf-Kappab Inducing Kinase (Nik) Bound to Inhibitor R7 within 5.0Å range: probe atom residue distance (Å) B Occ B:F704 b:45.9 occ:0.69 F17 B:K6Y704 0.0 45.9 0.7 C16 B:K6Y704 1.4 52.5 0.7 C15 B:K6Y704 2.3 48.4 0.7 C11 B:K6Y704 2.4 50.9 0.7 OD2 B:ASP536 2.8 49.7 1.0 C10 B:K6Y704 2.8 52.0 0.7 CG B:ASP536 2.9 54.5 1.0 CB B:ASP536 3.0 51.0 1.0 CE B:LYS431 3.5 41.9 1.0 NZ B:LYS431 3.6 46.4 1.0 C12 B:K6Y704 3.6 41.0 0.7 C14 B:K6Y704 3.6 50.5 0.7 C9 B:K6Y704 3.6 47.9 0.7 CD B:LYS431 3.6 39.8 1.0 OD1 B:ASP536 3.7 64.9 1.0 CA B:ASP536 3.7 43.4 1.0 OE2 B:GLU415 4.1 50.3 1.0 C13 B:K6Y704 4.1 47.3 0.7 N B:ASP536 4.4 44.6 1.0 CG B:LYS431 4.4 38.3 1.0 OD1 B:ASN522 4.6 52.6 1.0 CG2 B:VAL416 4.8 40.6 1.0 C7 B:K6Y704 4.8 49.2 0.7 C18 B:K6Y704 4.8 49.6 0.7 O34 B:K6Y704 4.9 46.8 0.7 C B:ASP536 4.9 42.8 1.0

J.A.Feng, P.Lee, M.H.Alaoui, K.Barrett, G.Castanedo, R.Godemann, P.Mcewan, X.Wang, P.Wu, Y.Zhang, S.F.Harris, S.T.Staben. Structure Based Design of Potent Selective Inhibitors of Protein Kinase D1 (PKD1). Acs Med.Chem.Lett. V. 10 1260 2019.
ISSN: ISSN 1948-5875
PubMed: 31531194
DOI: 10.1021/ACSMEDCHEMLETT.8B00658