Fluorine in PDB 6dmg: A Multiconformer Ligand Model of EK6 Bound to ERK2

All present enzymatic activity of A Multiconformer Ligand Model of EK6 Bound to ERK2:
2.7.11.24;

The structure of A Multiconformer Ligand Model of EK6 Bound to ERK2, PDB code: 6dmg was solved by B.M.Hudson, G.C.P.Van Zundert, D.A.Keedy, R.Fonseca, A.Heliou, P.Suresh, K.Borrelli, T.Day, J.S.Fraser, H.Van Den Bedem, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.93 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	48.780, 70.700, 60.860, 90.00, 110.11, 90.00
R / Rfree (%)	18.6 / 23.6

The structure of A Multiconformer Ligand Model of EK6 Bound to ERK2 also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Fluorine atom in the A Multiconformer Ligand Model of EK6 Bound to ERK2 (pdb code 6dmg). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the A Multiconformer Ligand Model of EK6 Bound to ERK2, PDB code: 6dmg:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the A Multiconformer Ligand Model of EK6 Bound to ERK2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of A Multiconformer Ligand Model of EK6 Bound to ERK2 within 5.0Å range: probe atom residue distance (Å) B Occ A:F407 b:52.1 occ:0.46 F A:EK6407 0.0 52.1 0.5 F A:EK6407 0.1 52.1 0.5 C22 A:EK6407 1.4 46.3 0.5 C22 A:EK6407 1.4 46.2 0.5 C23 A:EK6407 2.4 43.6 0.5 C21 A:EK6407 2.4 45.0 0.5 C21 A:EK6407 2.4 45.0 0.5 C23 A:EK6407 2.5 43.6 0.5 H26 A:EK6407 2.6 54.0 0.5 H26 A:EK6407 2.6 54.0 0.5 HA3 A:GLY32 2.9 65.6 1.0 HA3 A:GLY35 3.0 59.5 1.0 CL1 A:EK6407 3.0 50.6 0.5 CL1 A:EK6407 3.1 50.6 0.5 H A:TYR34 3.2 80.4 1.0 H A:GLY35 3.3 63.3 1.0 N A:GLY35 3.3 52.8 1.0 CA A:GLY35 3.5 49.6 1.0 HD2 A:LYS52 3.5 45.1 1.0 C20 A:EK6407 3.6 41.0 0.5 C24 A:EK6407 3.6 41.0 0.5 C20 A:EK6407 3.7 40.9 0.5 C24 A:EK6407 3.7 40.9 0.5 CA A:GLY32 3.8 54.7 1.0 H A:GLY32 3.9 65.2 1.0 C A:GLY35 3.9 47.5 1.0 C A:TYR34 3.9 56.4 1.0 H A:ALA33 4.0 73.0 1.0 O A:GLY35 4.0 49.9 1.0 N A:TYR34 4.0 67.0 1.0 CD2 A:TYR34 4.1 63.0 1.0 CE2 A:TYR34 4.1 65.9 1.0 C19 A:EK6407 4.1 39.6 0.5 C19 A:EK6407 4.2 39.7 0.5 C A:GLY32 4.2 58.0 1.0 N A:ALA33 4.2 60.9 1.0 HD2 A:TYR34 4.2 75.6 1.0 HE2 A:TYR34 4.3 79.1 1.0 N A:GLY32 4.3 54.4 1.0 H25 A:EK6407 4.4 49.2 0.5 H27 A:EK6407 4.4 49.2 0.5 HA2 A:GLY35 4.4 59.5 1.0 H27 A:EK6407 4.4 49.0 0.5 CD A:LYS52 4.4 37.6 1.0 HA2 A:GLY32 4.4 65.6 1.0 H25 A:EK6407 4.5 49.0 0.5 HG3 A:LYS52 4.5 46.9 1.0 CG A:TYR34 4.5 64.2 1.0 CZ A:TYR34 4.5 67.8 1.0 O A:TYR34 4.5 51.1 1.0 H9 A:EK6407 4.5 48.3 0.5 CA A:TYR34 4.5 62.3 1.0 HG12 A:ILE54 4.7 53.8 1.0 N A:MET36 4.7 49.6 1.0 HD3 A:LYS52 4.8 45.1 1.0 CD1 A:TYR34 4.8 60.1 1.0 CE1 A:TYR34 4.8 62.7 1.0 HZ2 A:LYS52 4.9 43.5 1.0 CG A:LYS52 4.9 39.1 1.0 HG2 A:LYS52 4.9 46.9 1.0 O A:GLY32 5.0 62.0 1.0 H A:MET36 5.0 59.5 1.0 HG23 A:ILE54 5.0 61.2 1.0

Fluorine binding site 2 out of 2 in the A Multiconformer Ligand Model of EK6 Bound to ERK2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of A Multiconformer Ligand Model of EK6 Bound to ERK2 within 5.0Å range: probe atom residue distance (Å) B Occ A:F407 b:52.1 occ:0.54 F A:EK6407 0.0 52.1 0.5 F A:EK6407 0.1 52.1 0.5 C22 A:EK6407 1.3 46.3 0.5 C22 A:EK6407 1.4 46.2 0.5 C23 A:EK6407 2.3 43.6 0.5 C21 A:EK6407 2.4 45.0 0.5 C21 A:EK6407 2.4 45.0 0.5 C23 A:EK6407 2.4 43.6 0.5 H26 A:EK6407 2.6 54.0 0.5 H26 A:EK6407 2.6 54.0 0.5 HA3 A:GLY32 2.8 65.6 1.0 CL1 A:EK6407 2.9 50.6 0.5 CL1 A:EK6407 3.0 50.6 0.5 HA3 A:GLY35 3.0 59.5 1.0 H A:TYR34 3.2 80.4 1.0 H A:GLY35 3.3 63.3 1.0 N A:GLY35 3.4 52.8 1.0 HD2 A:LYS52 3.5 45.1 1.0 CA A:GLY35 3.5 49.6 1.0 C24 A:EK6407 3.6 41.0 0.5 C20 A:EK6407 3.6 41.0 0.5 C20 A:EK6407 3.6 40.9 0.5 C24 A:EK6407 3.6 40.9 0.5 CA A:GLY32 3.7 54.7 1.0 H A:GLY32 3.8 65.2 1.0 C A:GLY35 3.9 47.5 1.0 H A:ALA33 4.0 73.0 1.0 O A:GLY35 4.0 49.9 1.0 C A:TYR34 4.0 56.4 1.0 N A:TYR34 4.1 67.0 1.0 C19 A:EK6407 4.1 39.6 0.5 CD2 A:TYR34 4.1 63.0 1.0 C19 A:EK6407 4.1 39.7 0.5 CE2 A:TYR34 4.1 65.9 1.0 C A:GLY32 4.1 58.0 1.0 N A:ALA33 4.2 60.9 1.0 N A:GLY32 4.2 54.4 1.0 HD2 A:TYR34 4.3 75.6 1.0 HE2 A:TYR34 4.3 79.1 1.0 H25 A:EK6407 4.3 49.2 0.5 HA2 A:GLY32 4.4 65.6 1.0 H27 A:EK6407 4.4 49.2 0.5 H27 A:EK6407 4.4 49.0 0.5 H25 A:EK6407 4.4 49.0 0.5 CD A:LYS52 4.4 37.6 1.0 HA2 A:GLY35 4.5 59.5 1.0 H9 A:EK6407 4.5 48.3 0.5 HG3 A:LYS52 4.5 46.9 1.0 CG A:TYR34 4.5 64.2 1.0 CZ A:TYR34 4.5 67.8 1.0 O A:TYR34 4.6 51.1 1.0 CA A:TYR34 4.6 62.3 1.0 N A:MET36 4.7 49.6 1.0 HG12 A:ILE54 4.8 53.8 1.0 HD3 A:LYS52 4.8 45.1 1.0 HZ2 A:LYS52 4.9 43.5 1.0 CG A:LYS52 4.9 39.1 1.0 CD1 A:TYR34 4.9 60.1 1.0 CE1 A:TYR34 4.9 62.7 1.0 HG2 A:LYS52 4.9 46.9 1.0 O A:GLY32 4.9 62.0 1.0 H A:MET36 5.0 59.5 1.0

G.C.P.Van Zundert, B.M.Hudson, S.H.P.De Oliveira, D.A.Keedy, R.Fonseca, A.Heliou, P.Suresh, K.Borrelli, T.Day, J.S.Fraser, H.Van Den Bedem. Qfit-Ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps. J. Med. Chem. V. 61 11183 2018.
ISSN: ISSN 1520-4804
PubMed: 30457858
DOI: 10.1021/ACS.JMEDCHEM.8B01292