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

Enzymatic activity of 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;

Protein crystallography data

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

Fluorine Binding Sites:

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 6myn

Go back to Fluorine Binding Sites List in 6myn
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 6myn

Go back to Fluorine Binding Sites List in 6myn
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

Reference:

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
Page generated: Sun Dec 13 12:59:09 2020

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