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Chlorine in PDB 6bmy: Non-Receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitors SHP099 and SHP844

Enzymatic activity of Non-Receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitors SHP099 and SHP844

All present enzymatic activity of Non-Receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitors SHP099 and SHP844:
3.1.3.48;

Protein crystallography data

The structure of Non-Receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitors SHP099 and SHP844, PDB code: 6bmy was solved by T.Stams, M.Fodor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 106.85 / 2.09
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 46.050, 213.710, 55.980, 90.00, 96.71, 90.00
R / Rfree (%) 18 / 22.8

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Non-Receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitors SHP099 and SHP844 (pdb code 6bmy). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Non-Receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitors SHP099 and SHP844, PDB code: 6bmy:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 6bmy

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Chlorine binding site 1 out of 6 in the Non-Receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitors SHP099 and SHP844


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Non-Receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitors SHP099 and SHP844 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl601

b:38.2
occ:1.00
 CL1 A:5OD601 0.0 38.2 1.0
C15 A:5OD601 1.8 32.0 1.0
C16 A:5OD601 2.7 31.3 1.0
C8 A:5OD601 2.7 31.7 1.0
C1 A:5OD601 3.1 35.1 1.0
CL2 A:5OD601 3.1 36.6 1.0
O A:THR253 3.3 32.8 1.0
N7 A:5OD601 3.3 33.2 1.0
C6 A:5OD601 3.4 36.4 1.0
CA A:LEU254 3.5 28.4 1.0
CD A:ARG111 3.5 48.7 0.5
CG A:ARG111 3.6 38.0 0.5
CD A:ARG111 3.6 37.9 0.5
CG A:GLN257 3.6 41.1 1.0
C A:THR253 3.6 33.5 1.0
N A:LEU254 3.7 29.3 1.0
CG2 A:THR253 3.9 27.4 1.0
N2 A:5OD601 4.0 36.4 1.0
C17 A:5OD601 4.0 27.8 1.0
CG A:ARG111 4.0 46.2 0.5
C19 A:5OD601 4.0 31.7 1.0
NE A:ARG111 4.3 33.5 0.5
O A:HOH737 4.3 34.8 1.0
CD1 A:LEU254 4.3 29.0 1.0
CB A:LEU254 4.3 27.4 1.0
N5 A:5OD601 4.4 37.5 1.0
CB A:GLN257 4.5 30.9 1.0
C18 A:5OD601 4.6 28.7 1.0
CB A:THR253 4.6 33.0 1.0
C A:LEU254 4.6 31.0 1.0
CA A:THR253 4.7 30.4 1.0
O A:LEU254 4.7 31.4 1.0
CD A:GLN257 4.8 48.0 1.0
NE A:ARG111 4.8 51.4 0.5
C3 A:5OD601 4.8 36.7 1.0
CZ A:ARG111 4.9 44.6 0.5
CG A:LEU254 5.0 29.9 1.0

Chlorine binding site 2 out of 6 in 6bmy

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Chlorine binding site 2 out of 6 in the Non-Receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitors SHP099 and SHP844


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Non-Receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitors SHP099 and SHP844 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl601

b:36.6
occ:1.00
 CL2 A:5OD601 0.0 36.6 1.0
C16 A:5OD601 1.7 31.3 1.0
C15 A:5OD601 2.7 32.0 1.0
C17 A:5OD601 2.7 27.8 1.0
CL1 A:5OD601 3.1 38.2 1.0
O A:HOH804 3.4 58.4 1.0
CD A:GLN495 3.5 42.8 1.0
CG A:GLN495 3.5 28.7 1.0
CG A:GLN257 3.6 41.1 1.0
CB A:GLN257 3.7 30.9 1.0
CD1 A:LEU254 3.7 29.0 1.0
CB A:GLN495 3.7 23.9 1.0
OE1 A:GLN495 3.8 39.1 1.0
C8 A:5OD601 4.0 31.7 1.0
C18 A:5OD601 4.0 28.7 1.0
NE2 A:GLN495 4.0 28.6 1.0
C19 A:5OD601 4.5 31.7 1.0
NH2 A:ARG111 4.6 29.1 0.5
CD A:ARG111 4.7 48.7 0.5
O A:PRO491 4.7 29.6 1.0
CD A:GLN257 4.7 48.0 1.0
CD A:ARG111 4.7 37.9 0.5
OE1 A:GLN257 4.8 43.9 1.0
CA A:LEU254 4.9 28.4 1.0
O A:LEU254 4.9 31.4 1.0

Chlorine binding site 3 out of 6 in 6bmy

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Chlorine binding site 3 out of 6 in the Non-Receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitors SHP099 and SHP844


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Non-Receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitors SHP099 and SHP844 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl602

b:36.2
occ:1.00
 CL1 A:DYV602 0.0 36.2 1.0
C23 A:DYV602 1.7 37.6 1.0
C22 A:DYV602 2.7 39.8 1.0
C18 A:DYV602 2.7 37.0 1.0
C17 A:DYV602 3.0 35.9 1.0
O A:ASN281 3.4 30.0 1.0
O A:HOH835 3.5 41.4 1.0
CA A:ASN281 3.5 31.3 1.0
CB A:ASN281 3.7 32.8 1.0
OD1 A:ASN281 3.7 31.7 1.0
C A:ASN281 3.8 31.6 1.0
CG A:ASN281 3.9 43.2 1.0
CD1 A:LEU283 3.9 30.8 1.0
CD1 A:TYR80 4.0 31.8 1.0
C19 A:DYV602 4.1 38.4 1.0
C21 A:DYV602 4.1 43.6 1.0
CE1 A:TYR80 4.5 32.0 1.0
N1 A:DYV602 4.5 35.3 1.0
CG A:LEU283 4.5 30.7 1.0
C20 A:DYV602 4.6 41.0 1.0
O A:LYS280 4.7 35.3 1.0
O A:HOH751 4.7 34.4 1.0
NH2 A:ARG265 4.7 24.0 1.0
CG A:TYR80 4.7 30.6 1.0
N A:ASN281 4.8 32.0 1.0
ND2 A:ASN281 4.8 31.5 1.0
CE1 A:PHE71 4.9 31.4 1.0
CB A:TYR80 5.0 31.1 1.0
O6 A:DYV602 5.0 37.1 1.0

Chlorine binding site 4 out of 6 in 6bmy

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Chlorine binding site 4 out of 6 in the Non-Receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitors SHP099 and SHP844


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Non-Receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitors SHP099 and SHP844 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl601

b:37.7
occ:1.00
 CL1 B:5OD601 0.0 37.7 1.0
C15 B:5OD601 1.7 36.0 1.0
C16 B:5OD601 2.7 32.6 1.0
C8 B:5OD601 2.7 36.9 1.0
CL2 B:5OD601 3.0 38.4 1.0
C1 B:5OD601 3.1 37.5 1.0
O B:THR253 3.3 31.8 1.0
C6 B:5OD601 3.4 36.6 1.0
N7 B:5OD601 3.4 32.6 1.0
CG B:ARG111 3.5 41.9 1.0
CG B:GLN257 3.5 37.3 1.0
CD B:ARG111 3.6 51.4 1.0
CA B:LEU254 3.6 28.9 1.0
C B:THR253 3.7 32.5 1.0
N B:LEU254 3.8 30.1 1.0
C17 B:5OD601 4.0 29.4 1.0
N2 B:5OD601 4.0 38.5 1.0
CG2 B:THR253 4.0 34.4 1.0
C19 B:5OD601 4.0 34.3 1.0
O B:HOH795 4.2 45.9 1.0
CB B:GLN257 4.4 30.1 1.0
CB B:LEU254 4.4 28.2 1.0
CD1 B:LEU254 4.5 31.0 1.0
N5 B:5OD601 4.5 38.7 1.0
C18 B:5OD601 4.5 30.7 1.0
CB B:THR253 4.6 35.7 1.0
C B:LEU254 4.7 29.7 1.0
CD B:GLN257 4.7 45.1 1.0
CA B:THR253 4.7 28.7 1.0
O B:LEU254 4.7 29.0 1.0
O B:HOH797 4.8 54.5 1.0
NE B:ARG111 4.9 60.6 1.0
C3 B:5OD601 4.9 39.6 1.0
CB B:PRO491 5.0 31.8 1.0

Chlorine binding site 5 out of 6 in 6bmy

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Chlorine binding site 5 out of 6 in the Non-Receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitors SHP099 and SHP844


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Non-Receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitors SHP099 and SHP844 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl601

b:38.4
occ:1.00
 CL2 B:5OD601 0.0 38.4 1.0
C16 B:5OD601 1.7 32.6 1.0
C15 B:5OD601 2.7 36.0 1.0
C17 B:5OD601 2.7 29.4 1.0
CL1 B:5OD601 3.0 37.7 1.0
CG B:GLN495 3.6 26.9 1.0
CG B:GLN257 3.6 37.3 1.0
CD B:GLN495 3.6 36.7 1.0
CB B:GLN257 3.7 30.1 1.0
CB B:GLN495 3.7 24.6 1.0
CD1 B:LEU254 3.8 31.0 1.0
O B:HOH923 3.8 41.5 1.0
O B:HOH854 3.8 68.4 1.0
OE1 B:GLN495 3.9 29.8 1.0
C8 B:5OD601 4.0 36.9 1.0
C18 B:5OD601 4.0 30.7 1.0
NE2 B:GLN495 4.2 22.5 1.0
NH2 B:ARG111 4.5 76.5 1.0
C19 B:5OD601 4.6 34.3 1.0
O B:PRO491 4.7 27.8 1.0
CD B:ARG111 4.7 51.4 1.0
CD B:GLN257 4.8 45.1 1.0
CA B:LEU254 4.9 28.9 1.0
O B:LEU254 4.9 29.0 1.0
OE1 B:GLN257 5.0 40.9 1.0

Chlorine binding site 6 out of 6 in 6bmy

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Chlorine binding site 6 out of 6 in the Non-Receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitors SHP099 and SHP844


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Non-Receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitors SHP099 and SHP844 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl602

b:37.4
occ:1.00
 CL1 B:DYV602 0.0 37.4 1.0
C23 B:DYV602 1.7 39.6 1.0
C22 B:DYV602 2.7 41.2 1.0
C18 B:DYV602 2.7 36.9 1.0
C17 B:DYV602 3.0 31.7 1.0
O B:HOH775 3.2 27.2 1.0
O B:ASN281 3.3 30.3 1.0
CA B:ASN281 3.5 28.0 1.0
CB B:ASN281 3.6 26.0 1.0
ND2 B:ASN281 3.7 25.1 1.0
C B:ASN281 3.8 30.8 1.0
CD1 B:LEU283 3.8 29.5 1.0
CD2 B:TYR80 3.9 32.8 1.0
CG B:ASN281 3.9 35.6 1.0
C21 B:DYV602 4.0 47.8 1.0
C19 B:DYV602 4.1 41.6 1.0
CE2 B:TYR80 4.4 33.5 1.0
N1 B:DYV602 4.5 30.8 1.0
CG B:LEU283 4.5 29.2 1.0
C20 B:DYV602 4.5 44.6 1.0
NH1 B:ARG265 4.7 20.3 1.0
CG B:TYR80 4.7 33.0 1.0
O B:HOH770 4.8 33.0 1.0
O B:LYS280 4.8 28.4 1.0
CE1 B:PHE71 4.8 32.4 1.0
N B:ASN281 4.8 29.0 1.0
OD1 B:ASN281 4.9 37.6 1.0
O6 B:DYV602 5.0 30.2 1.0
N B:ILE282 5.0 25.8 1.0
CB B:TYR80 5.0 31.3 1.0

Reference:

M.Fodor, E.Price, P.Wang, H.Lu, A.Argintaru, Z.Chen, M.Glick, H.X.Hao, M.Kato, R.Koenig, J.R.Larochelle, G.Liu, E.Mcneill, D.Majumdar, G.A.Nishiguchi, L.B.Perez, G.Paris, C.M.Quinn, T.Ramsey, M.Sendzik, M.D.Shultz, S.L.Williams, T.Stams, S.C.Blacklow, M.G.Acker, M.J.Lamarche. Dual Allosteric Inhibition of SHP2 Phosphatase. Acs Chem. Biol. V. 13 647 2018.
ISSN: ESSN 1554-8937
PubMed: 29304282
DOI: 10.1021/ACSCHEMBIO.7B00980
Page generated: Sat Jul 12 11:58:48 2025

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