Chlorine 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:

Fluorine

(F)

2 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 4 binding sites of Chlorine where determined in the A Multiconformer Ligand Model of EK6 Bound to ERK2, PDB code: 6dmg:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the A Multiconformer Ligand Model of EK6 Bound to ERK2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl407 b:37.5 occ:0.46 CL2 A:EK6407 0.0 37.5 0.5 CL2 A:EK6407 0.2 37.7 0.5 C27 A:EK6407 1.6 34.3 0.5 C27 A:EK6407 1.8 33.7 0.5 C26 A:EK6407 2.6 33.0 0.5 C6 A:EK6407 2.6 33.3 0.5 H1 A:EK6407 2.6 41.5 0.5 H12 A:EK6407 2.7 39.6 0.5 H3 A:EK6407 2.7 42.3 0.5 C6 A:EK6407 2.8 33.2 0.5 C26 A:EK6407 2.8 33.1 0.5 HA3 A:GLY30 2.8 57.3 1.0 H12 A:EK6407 2.8 39.7 0.5 H2 A:EK6407 2.9 41.3 0.5 C5 A:EK6407 2.9 34.6 0.5 HB A:VAL37 3.0 49.6 1.0 C5 A:EK6407 3.1 34.4 0.5 N1 A:EK6407 3.1 35.3 0.5 HG21 A:VAL37 3.2 44.1 1.0 N1 A:EK6407 3.3 35.4 0.5 HG23 A:VAL37 3.4 44.1 1.0 H25 A:EK6407 3.4 49.2 0.5 H25 A:EK6407 3.4 49.0 0.5 CA A:GLY30 3.5 47.8 1.0 CG2 A:VAL37 3.6 36.8 1.0 C A:GLY30 3.7 46.7 1.0 CB A:VAL37 3.7 41.3 1.0 H A:GLY30 3.8 52.9 1.0 C7 A:EK6407 3.8 32.0 0.5 C9 A:EK6407 3.8 32.3 0.5 O1 A:EK6407 3.9 38.8 0.5 H2 A:EK6407 3.9 41.5 0.5 H3 A:EK6407 3.9 42.5 0.5 N A:GLY30 3.9 44.0 1.0 HG22 A:ILE29 4.0 48.1 1.0 CL1 A:EK6407 4.0 50.6 0.5 O A:HOH546 4.0 32.4 1.0 H1 A:EK6407 4.0 41.3 0.5 C7 A:EK6407 4.0 32.0 0.5 C9 A:EK6407 4.0 32.1 0.5 O A:GLY30 4.1 50.0 1.0 CL1 A:EK6407 4.1 50.6 0.5 C3 A:EK6407 4.1 37.4 0.5 N A:GLU31 4.2 50.3 1.0 C4 A:EK6407 4.2 37.1 0.5 H20 A:EK6407 4.2 42.3 0.5 HG11 A:VAL37 4.2 47.0 1.0 H20 A:EK6407 4.3 41.9 0.5 C24 A:EK6407 4.3 40.9 0.5 H17 A:EK6407 4.3 38.5 0.5 C24 A:EK6407 4.3 41.0 0.5 H A:GLU31 4.3 60.4 1.0 C8 A:EK6407 4.3 31.9 0.5 HA2 A:GLY30 4.4 57.3 1.0 H A:VAL37 4.4 52.7 1.0 H17 A:EK6407 4.4 38.4 0.5 C4 A:EK6407 4.5 35.9 0.5 HG22 A:VAL37 4.5 44.1 1.0 H5 A:EK6407 4.5 44.5 0.5 C8 A:EK6407 4.6 31.7 0.5 H14 A:EK6407 4.6 38.4 0.5 CG1 A:VAL37 4.6 39.2 1.0 HB A:ILE29 4.6 56.1 1.0 HG21 A:ILE29 4.7 48.1 1.0 C23 A:EK6407 4.7 43.6 0.5 CG2 A:ILE29 4.7 40.1 1.0 O2 A:EK6407 4.7 40.2 0.5 O2 A:EK6407 4.7 36.1 0.5 C23 A:EK6407 4.7 43.6 0.5 C25 A:EK6407 4.8 32.1 0.5 H14 A:EK6407 4.8 38.4 0.5 N5 A:EK6407 4.8 35.3 0.5 C25 A:EK6407 4.8 32.0 0.5 H5 A:EK6407 4.8 43.1 0.5 N A:VAL37 4.8 43.9 1.0 N5 A:EK6407 4.9 34.9 0.5 CA A:VAL37 4.9 44.5 1.0 C A:ILE29 4.9 44.6 1.0 HA A:GLU31 4.9 64.5 1.0 H22 A:EK6407 5.0 43.2 0.5 HG12 A:VAL37 5.0 47.0 1.0 H23 A:EK6407 5.0 42.9 0.5

Chlorine binding site 2 out of 4 in the A Multiconformer Ligand Model of EK6 Bound to ERK2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl407 b:37.7 occ:0.54 CL2 A:EK6407 0.0 37.7 0.5 CL2 A:EK6407 0.2 37.5 0.5 C27 A:EK6407 1.8 34.3 0.5 C27 A:EK6407 2.0 33.7 0.5 H1 A:EK6407 2.7 41.5 0.5 H3 A:EK6407 2.7 42.3 0.5 C26 A:EK6407 2.8 33.0 0.5 C6 A:EK6407 2.8 33.3 0.5 HA3 A:GLY30 2.8 57.3 1.0 H12 A:EK6407 2.8 39.6 0.5 C26 A:EK6407 3.0 33.1 0.5 C6 A:EK6407 3.0 33.2 0.5 H12 A:EK6407 3.0 39.7 0.5 H2 A:EK6407 3.0 41.3 0.5 HB A:VAL37 3.0 49.6 1.0 C5 A:EK6407 3.1 34.6 0.5 HG21 A:VAL37 3.1 44.1 1.0 N1 A:EK6407 3.1 35.3 0.5 C5 A:EK6407 3.2 34.4 0.5 HG23 A:VAL37 3.3 44.1 1.0 H25 A:EK6407 3.3 49.2 0.5 H25 A:EK6407 3.3 49.0 0.5 N1 A:EK6407 3.4 35.4 0.5 CG2 A:VAL37 3.5 36.8 1.0 CA A:GLY30 3.5 47.8 1.0 C A:GLY30 3.6 46.7 1.0 O1 A:EK6407 3.7 38.8 0.5 CB A:VAL37 3.7 41.3 1.0 CL1 A:EK6407 3.7 50.6 0.5 CL1 A:EK6407 3.8 50.6 0.5 H A:GLY30 3.9 52.9 1.0 O A:GLY30 4.0 50.0 1.0 C3 A:EK6407 4.0 37.4 0.5 H2 A:EK6407 4.0 41.5 0.5 H3 A:EK6407 4.0 42.5 0.5 N A:GLY30 4.0 44.0 1.0 N A:GLU31 4.0 50.3 1.0 C7 A:EK6407 4.0 32.0 0.5 C9 A:EK6407 4.0 32.3 0.5 O A:HOH546 4.1 32.4 1.0 C24 A:EK6407 4.1 40.9 0.5 C24 A:EK6407 4.1 41.0 0.5 HG22 A:ILE29 4.2 48.1 1.0 H1 A:EK6407 4.2 41.3 0.5 H A:GLU31 4.2 60.4 1.0 H20 A:EK6407 4.2 42.3 0.5 C4 A:EK6407 4.2 37.1 0.5 C9 A:EK6407 4.3 32.1 0.5 H20 A:EK6407 4.3 41.9 0.5 C7 A:EK6407 4.3 32.0 0.5 H A:VAL37 4.3 52.7 1.0 HG11 A:VAL37 4.3 47.0 1.0 HA2 A:GLY30 4.4 57.3 1.0 H17 A:EK6407 4.4 38.5 0.5 HG22 A:VAL37 4.4 44.1 1.0 C23 A:EK6407 4.5 43.6 0.5 H17 A:EK6407 4.5 38.4 0.5 C23 A:EK6407 4.5 43.6 0.5 H5 A:EK6407 4.5 44.5 0.5 C4 A:EK6407 4.6 35.9 0.5 C8 A:EK6407 4.6 31.9 0.5 O2 A:EK6407 4.6 40.2 0.5 CG1 A:VAL37 4.6 39.2 1.0 O2 A:EK6407 4.7 36.1 0.5 N A:VAL37 4.7 43.9 1.0 HB A:ILE29 4.7 56.1 1.0 HA A:GLU31 4.8 64.5 1.0 H14 A:EK6407 4.8 38.4 0.5 C8 A:EK6407 4.8 31.7 0.5 N5 A:EK6407 4.8 35.3 0.5 CA A:VAL37 4.8 44.5 1.0 N5 A:EK6407 4.8 34.9 0.5 C25 A:EK6407 4.8 32.1 0.5 CA A:GLU31 4.9 53.8 1.0 HG21 A:ILE29 4.9 48.1 1.0 H5 A:EK6407 4.9 43.1 0.5 H23 A:EK6407 4.9 42.9 0.5 H22 A:EK6407 4.9 43.2 0.5 CG2 A:ILE29 4.9 40.1 1.0 C25 A:EK6407 4.9 32.0 0.5 C A:GLU31 5.0 55.2 1.0 C2 A:EK6407 5.0 38.6 0.5 H14 A:EK6407 5.0 38.4 0.5

Chlorine binding site 3 out of 4 in the A Multiconformer Ligand Model of EK6 Bound to ERK2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of A Multiconformer Ligand Model of EK6 Bound to ERK2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl407 b:50.6 occ:0.46 CL1 A:EK6407 0.0 50.6 0.5 CL1 A:EK6407 0.1 50.6 0.5 C23 A:EK6407 1.8 43.6 0.5 C23 A:EK6407 1.8 43.6 0.5 H A:GLY32 2.7 65.2 1.0 C22 A:EK6407 2.7 46.2 0.5 C24 A:EK6407 2.8 41.0 0.5 C22 A:EK6407 2.8 46.3 0.5 HA3 A:GLY32 2.8 65.6 1.0 C24 A:EK6407 2.8 40.9 0.5 HG23 A:VAL37 2.8 44.1 1.0 H25 A:EK6407 2.8 49.2 0.5 H25 A:EK6407 2.9 49.0 0.5 F A:EK6407 2.9 52.1 0.5 N A:GLY32 3.0 54.4 1.0 F A:EK6407 3.0 52.1 0.5 CA A:GLY32 3.3 54.7 1.0 O A:GLY35 3.4 49.9 1.0 HA A:MET36 3.5 62.3 1.0 HA A:GLU31 3.6 64.5 1.0 C A:GLY35 3.6 47.5 1.0 CG2 A:VAL37 3.7 36.8 1.0 C A:GLU31 3.7 55.2 1.0 HA2 A:GLY32 3.8 65.6 1.0 CL2 A:EK6407 3.8 37.7 0.5 HG21 A:VAL37 3.9 44.1 1.0 N A:MET36 3.9 49.6 1.0 HG3 A:LYS52 4.0 46.9 1.0 C21 A:EK6407 4.0 45.0 0.5 C19 A:EK6407 4.0 39.6 0.5 C21 A:EK6407 4.0 45.0 0.5 CA A:MET36 4.1 51.9 1.0 CL2 A:EK6407 4.1 37.5 0.5 HD2 A:LYS52 4.1 45.1 1.0 C19 A:EK6407 4.1 39.7 0.5 HG22 A:VAL37 4.1 44.1 1.0 CA A:GLU31 4.1 53.8 1.0 HA3 A:GLY35 4.1 59.5 1.0 O1 A:EK6407 4.2 38.8 0.5 H A:VAL37 4.2 52.7 1.0 C A:MET36 4.3 47.6 1.0 N A:VAL37 4.3 43.9 1.0 CA A:GLY35 4.4 49.6 1.0 H9 A:EK6407 4.4 48.3 0.5 HD3 A:LYS52 4.4 45.1 1.0 H A:GLY35 4.4 63.3 1.0 H A:MET36 4.5 59.5 1.0 N A:GLU31 4.5 50.3 1.0 C20 A:EK6407 4.6 41.0 0.5 O A:GLU31 4.6 57.9 1.0 CD A:LYS52 4.6 37.6 1.0 C20 A:EK6407 4.6 40.9 0.5 C A:GLY32 4.6 58.0 1.0 O A:GLY30 4.6 50.0 1.0 CG A:LYS52 4.7 39.1 1.0 HB A:VAL37 4.7 49.6 1.0 H26 A:EK6407 4.8 54.0 0.5 C A:GLY30 4.8 46.7 1.0 N A:GLY35 4.8 52.8 1.0 H7 A:EK6407 4.8 46.3 0.5 H26 A:EK6407 4.8 54.0 0.5 CB A:VAL37 4.8 41.3 1.0 C2 A:EK6407 4.9 38.6 0.5 O A:MET36 5.0 43.8 1.0 H A:GLU31 5.0 60.4 1.0

Chlorine binding site 4 out of 4 in the A Multiconformer Ligand Model of EK6 Bound to ERK2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of A Multiconformer Ligand Model of EK6 Bound to ERK2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl407 b:50.6 occ:0.54 CL1 A:EK6407 0.0 50.6 0.5 CL1 A:EK6407 0.1 50.6 0.5 C23 A:EK6407 1.8 43.6 0.5 C23 A:EK6407 1.8 43.6 0.5 H A:GLY32 2.7 65.2 1.0 C24 A:EK6407 2.7 41.0 0.5 C24 A:EK6407 2.8 40.9 0.5 H25 A:EK6407 2.8 49.2 0.5 C22 A:EK6407 2.8 46.2 0.5 C22 A:EK6407 2.8 46.3 0.5 HA3 A:GLY32 2.8 65.6 1.0 HG23 A:VAL37 2.8 44.1 1.0 H25 A:EK6407 2.8 49.0 0.5 N A:GLY32 3.0 54.4 1.0 F A:EK6407 3.0 52.1 0.5 F A:EK6407 3.1 52.1 0.5 CA A:GLY32 3.3 54.7 1.0 O A:GLY35 3.5 49.9 1.0 HA A:MET36 3.6 62.3 1.0 HA A:GLU31 3.6 64.5 1.0 C A:GLU31 3.7 55.2 1.0 CG2 A:VAL37 3.7 36.8 1.0 CL2 A:EK6407 3.7 37.7 0.5 C A:GLY35 3.7 47.5 1.0 HA2 A:GLY32 3.8 65.6 1.0 HG21 A:VAL37 3.8 44.1 1.0 CL2 A:EK6407 4.0 37.5 0.5 C19 A:EK6407 4.0 39.6 0.5 HG3 A:LYS52 4.0 46.9 1.0 C19 A:EK6407 4.0 39.7 0.5 C21 A:EK6407 4.0 45.0 0.5 C21 A:EK6407 4.1 45.0 0.5 N A:MET36 4.1 49.6 1.0 O1 A:EK6407 4.1 38.8 0.5 CA A:GLU31 4.1 53.8 1.0 HG22 A:VAL37 4.1 44.1 1.0 HD2 A:LYS52 4.1 45.1 1.0 CA A:MET36 4.1 51.9 1.0 H A:VAL37 4.2 52.7 1.0 HA3 A:GLY35 4.2 59.5 1.0 H9 A:EK6407 4.3 48.3 0.5 C A:MET36 4.4 47.6 1.0 N A:VAL37 4.4 43.9 1.0 HD3 A:LYS52 4.4 45.1 1.0 CA A:GLY35 4.5 49.6 1.0 N A:GLU31 4.5 50.3 1.0 O A:GLU31 4.5 57.9 1.0 H A:GLY35 4.5 63.3 1.0 C20 A:EK6407 4.5 41.0 0.5 C20 A:EK6407 4.6 40.9 0.5 O A:GLY30 4.6 50.0 1.0 H A:MET36 4.6 59.5 1.0 C A:GLY32 4.6 58.0 1.0 CD A:LYS52 4.6 37.6 1.0 H7 A:EK6407 4.7 46.3 0.5 HB A:VAL37 4.7 49.6 1.0 C A:GLY30 4.7 46.7 1.0 H26 A:EK6407 4.8 54.0 0.5 CB A:VAL37 4.8 41.3 1.0 H26 A:EK6407 4.8 54.0 0.5 CG A:LYS52 4.8 39.1 1.0 C2 A:EK6407 4.8 38.6 0.5 N A:GLY35 4.9 52.8 1.0 H A:GLU31 4.9 60.4 1.0 C1 A:EK6407 5.0 40.3 0.5

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