Chlorine in PDB 6cmr: Closed Structure of Active SHP2 Mutant E76D Bound to SHP099 Inhibitor

All present enzymatic activity of Closed Structure of Active SHP2 Mutant E76D Bound to SHP099 Inhibitor:
3.1.3.48;

The structure of Closed Structure of Active SHP2 Mutant E76D Bound to SHP099 Inhibitor, PDB code: 6cmr was solved by R.A.P.Padua, Y.Sun, I.Marko, W.Pitsawong, D.Kern, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.79 / 2.21
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	41.270, 54.360, 221.530, 90.00, 90.00, 90.00
R / Rfree (%)	22.4 / 26.1

The binding sites of Chlorine atom in the Closed Structure of Active SHP2 Mutant E76D Bound to SHP099 Inhibitor (pdb code 6cmr). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Closed Structure of Active SHP2 Mutant E76D Bound to SHP099 Inhibitor, PDB code: 6cmr:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Closed Structure of Active SHP2 Mutant E76D Bound to SHP099 Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Closed Structure of Active SHP2 Mutant E76D Bound to SHP099 Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl601 b:37.8 occ:1.00 CL1 A:5OD601 0.0 37.8 1.0 C15 A:5OD601 1.8 37.8 1.0 H15 A:5OD601 2.3 53.3 1.0 HD2 A:ARG111 2.7 54.3 1.0 HG22 A:THR253 2.7 57.7 1.0 C16 A:5OD601 2.7 39.8 1.0 C8 A:5OD601 2.8 40.7 1.0 HA A:LEU254 2.8 51.1 1.0 HG2 A:ARG111 2.8 54.0 1.0 N7 A:5OD601 2.8 44.4 1.0 HG3 A:GLN257 3.0 53.2 1.0 C1 A:5OD601 3.1 44.4 1.0 C6 A:5OD601 3.2 42.9 1.0 CL2 A:5OD601 3.2 39.6 1.0 O A:THR253 3.2 45.4 1.0 CD A:ARG111 3.4 45.3 1.0 CG A:ARG111 3.4 45.1 1.0 HG2 A:GLN257 3.4 53.2 1.0 H14 A:5OD601 3.5 53.3 1.0 HG3 A:ARG111 3.6 54.0 1.0 CA A:LEU254 3.6 42.6 1.0 CG A:GLN257 3.6 44.3 1.0 CG2 A:THR253 3.6 48.1 1.0 C A:THR253 3.7 44.9 1.0 HG23 A:THR253 3.7 57.7 1.0 HD12 A:LEU254 3.8 51.1 1.0 N A:LEU254 3.8 44.2 1.0 NE A:ARG111 3.8 45.4 1.0 HD13 A:LEU254 3.8 51.1 1.0 HB2 A:LEU254 3.9 50.8 1.0 HE A:ARG111 3.9 54.3 1.0 C17 A:5OD601 4.0 42.8 1.0 C19 A:5OD601 4.1 44.9 1.0 HE21 A:GLN257 4.1 56.1 1.0 N2 A:5OD601 4.1 45.9 1.0 HG21 A:THR253 4.1 57.7 1.0 N5 A:5OD601 4.2 44.7 1.0 HD3 A:ARG111 4.2 54.3 1.0 CD1 A:LEU254 4.2 42.6 1.0 CB A:LEU254 4.3 42.3 1.0 H A:LEU254 4.3 53.1 1.0 HB2 A:PRO491 4.4 47.6 1.0 CD A:GLN257 4.4 47.2 1.0 NE2 A:GLN257 4.5 46.9 1.0 CZ A:ARG111 4.5 45.8 1.0 HB A:THR253 4.5 57.0 1.0 CB A:THR253 4.5 47.4 1.0 C18 A:5OD601 4.6 42.5 1.0 HH11 A:ARG111 4.6 57.8 1.0 HB2 A:GLN257 4.6 51.7 1.0 CA A:THR253 4.7 46.9 1.0 C A:LEU254 4.7 43.4 1.0 H8 A:5OD601 4.8 51.4 1.0 CB A:ARG111 4.8 45.2 1.0 H10 A:5OD601 4.8 53.9 1.0 CB A:GLN257 4.8 43.2 1.0 NH1 A:ARG111 4.8 48.1 1.0 O A:LEU254 4.9 43.5 1.0 CG A:LEU254 4.9 43.0 1.0 HB3 A:ARG111 4.9 54.1 1.0 C3 A:5OD601 5.0 44.8 1.0 HB3 A:PRO491 5.0 47.6 1.0 C4 A:5OD601 5.0 46.2 1.0

Chlorine binding site 2 out of 2 in the Closed Structure of Active SHP2 Mutant E76D Bound to SHP099 Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Closed Structure of Active SHP2 Mutant E76D Bound to SHP099 Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl601 b:39.6 occ:1.00 CL2 A:5OD601 0.0 39.6 1.0 C16 A:5OD601 1.8 39.8 1.0 C17 A:5OD601 2.7 42.8 1.0 C15 A:5OD601 2.8 37.8 1.0 HG3 A:GLN257 2.8 53.2 1.0 H8 A:5OD601 2.8 51.4 1.0 HD12 A:LEU254 2.9 51.1 1.0 HG2 A:GLN495 3.0 46.2 1.0 HB2 A:GLN495 3.2 49.0 1.0 CL1 A:5OD601 3.2 37.8 1.0 HD13 A:LEU254 3.3 51.1 1.0 CD1 A:LEU254 3.4 42.6 1.0 CD A:GLN495 3.5 39.0 1.0 HB2 A:GLN257 3.5 51.7 1.0 CG A:GLN495 3.5 38.6 1.0 HD2 A:ARG111 3.6 54.3 1.0 HD11 A:LEU254 3.6 51.1 1.0 CG A:GLN257 3.7 44.3 1.0 OE1 A:GLN495 3.7 38.5 1.0 CB A:GLN495 3.8 40.8 1.0 HH11 A:ARG111 3.9 57.8 1.0 NE2 A:GLN495 3.9 40.1 1.0 CB A:GLN257 3.9 43.2 1.0 HB3 A:GLN257 4.0 51.7 1.0 HA A:LEU254 4.0 51.1 1.0 HB3 A:GLN495 4.0 49.0 1.0 C18 A:5OD601 4.0 42.5 1.0 C8 A:5OD601 4.1 40.7 1.0 HG2 A:GLN257 4.1 53.2 1.0 HE21 A:GLN495 4.1 48.0 1.0 NH1 A:ARG111 4.1 48.1 1.0 O A:HOH779 4.1 42.5 1.0 HE22 A:GLN495 4.2 48.0 1.0 HH12 A:ARG111 4.4 57.8 1.0 HG3 A:GLN495 4.5 46.2 1.0 CD A:ARG111 4.5 45.3 1.0 C19 A:5OD601 4.5 44.9 1.0 CZ A:ARG111 4.6 45.8 1.0 HB2 A:PRO491 4.7 47.6 1.0 NE A:ARG111 4.7 45.4 1.0 H9 A:5OD601 4.8 51.1 1.0 CD A:GLN257 4.8 47.2 1.0 CG A:LEU254 4.8 43.0 1.0 H15 A:5OD601 4.8 53.3 1.0 CA A:LEU254 4.9 42.6 1.0 O A:PRO491 4.9 38.4 1.0 HA A:LYS492 4.9 47.5 1.0 O A:LEU254 5.0 43.5 1.0 HD3 A:ARG111 5.0 54.3 1.0

R.A.P.Padua, Y.Sun, I.Marko, W.Pitsawong, J.B.Stiller, R.Otten, D.Kern. Mechanism of Activating Mutations and Allosteric Drug Inhibition of the Phosphatase SHP2. Nat Commun V. 9 4507 2018.
ISSN: ESSN 2041-1723
PubMed: 30375376
DOI: 10.1038/S41467-018-06814-W