Fluorine in PDB 6wpp: Human Nik in Complex with Ligand Compound X

All present enzymatic activity of Human Nik in Complex with Ligand Compound X:
2.7.11.25;

The structure of Human Nik in Complex with Ligand Compound X, PDB code: 6wpp was solved by A.Y.Shih, M.Hack, T.Mirzadegan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	73.00 / 2.55
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.483, 81.521, 78.420, 90.00, 111.43, 90.00
R / Rfree (%)	20.5 / 25.6

The binding sites of Fluorine atom in the Human Nik in Complex with Ligand Compound X (pdb code 6wpp). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Human Nik in Complex with Ligand Compound X, PDB code: 6wpp:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Human Nik in Complex with Ligand Compound X


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human Nik in Complex with Ligand Compound X within 5.0Å range: probe atom residue distance (Å) B Occ A:F701 b:44.8 occ:1.00 F9 A:PZ4701 0.0 44.8 1.0 C8 A:PZ4701 1.3 39.2 1.0 C7 A:PZ4701 2.4 35.9 1.0 C3 A:PZ4701 2.4 36.0 1.0 N2 A:PZ4701 2.8 38.8 1.0 CG A:ASP534 2.9 42.9 1.0 OD2 A:ASP534 3.1 41.9 1.0 CB A:ASP534 3.2 40.2 1.0 OD1 A:ASP534 3.4 41.8 1.0 CA A:GLY409 3.5 67.4 1.0 CA A:ASP534 3.5 37.2 1.0 N6 A:PZ4701 3.6 33.7 1.0 N4 A:PZ4701 3.6 36.1 1.0 NZ A:LYS429 3.7 53.2 1.0 CD A:LYS429 3.8 46.1 1.0 CE A:LYS429 3.9 52.6 1.0 C5 A:PZ4701 4.1 34.3 1.0 N A:ASP534 4.1 36.6 1.0 C1 A:PZ4701 4.2 33.9 1.0 CG2 A:VAL414 4.2 39.2 1.0 N A:GLY409 4.4 64.8 1.0 N A:SER410 4.5 77.1 1.0 C A:GLY409 4.6 72.3 1.0 O A:HOH836 4.6 40.2 1.0 C A:ASP534 4.8 35.2 1.0 CG A:LYS429 4.9 40.1 1.0 O A:HOH801 5.0 29.6 1.0

Fluorine binding site 2 out of 2 in the Human Nik in Complex with Ligand Compound X


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human Nik in Complex with Ligand Compound X within 5.0Å range: probe atom residue distance (Å) B Occ B:F701 b:38.7 occ:0.50 F9 B:PZ4701 0.0 38.7 0.5 C8 B:PZ4701 1.3 38.7 0.5 C7 B:PZ4701 2.4 36.3 0.5 C3 B:PZ4701 2.4 41.9 0.5 N2 B:PZ4701 2.8 44.0 0.5 CG B:ASP534 3.0 48.1 1.0 OD2 B:ASP534 3.1 46.3 1.0 CB B:ASP534 3.2 45.2 1.0 CD B:LYS429 3.3 52.1 1.0 OD1 B:ASP534 3.4 45.0 1.0 NZ B:LYS429 3.5 47.0 1.0 N6 B:PZ4701 3.6 39.2 0.5 N4 B:PZ4701 3.6 42.2 0.5 CA B:GLY409 3.7 0.2 1.0 CA B:ASP534 3.9 39.1 1.0 CG2 B:VAL414 3.9 63.7 1.0 CE B:LYS429 4.0 49.8 1.0 C5 B:PZ4701 4.0 39.3 0.5 C1 B:PZ4701 4.2 43.1 0.5 N B:SER410 4.4 0.6 1.0 N B:ASP534 4.5 40.5 1.0 C B:GLY409 4.5 0.1 1.0 CG B:LYS429 4.6 50.0 1.0 OD1 B:ASN520 4.7 30.2 1.0 N B:GLY409 4.8 0.1 1.0 SG B:CYS533 4.9 48.2 1.0

A.Y.Shih, M.Hack, T.Mirzadegan. Impact of Protein Preparation on Resulting Accuracy of Fep Calculations. J.Chem.Inf.Model. V. 60 5287 2020.
ISSN: ESSN 1549-960X
PubMed: 32786514
DOI: 10.1021/ACS.JCIM.0C00445