Chlorine in PDB 6mdb: Non-Receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor Pyrazolo-Pyrimidinone 5

Enzymatic activity of Non-Receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor Pyrazolo-Pyrimidinone 5

All present enzymatic activity of Non-Receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor Pyrazolo-Pyrimidinone 5:
3.1.3.48;

Protein crystallography data

The structure of Non-Receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor Pyrazolo-Pyrimidinone 5, PDB code: 6mdb was solved by M.Fodor, T.Stams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.59 / 2.34
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 46.270, 213.520, 55.760, 90.00, 96.43, 90.00
R / Rfree (%) 17.5 / 23.6

Chlorine Binding Sites:

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

Chlorine binding site 1 out of 4 in 6mdb

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Chlorine binding site 1 out of 4 in the Non-Receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor Pyrazolo-Pyrimidinone 5


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 Inhibitor Pyrazolo-Pyrimidinone 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl601

b:67.6
occ:1.00
 CL1 A:JE4601 0.0 67.6 1.0
C15 A:JE4601 1.7 57.3 1.0
C14 A:JE4601 2.7 56.5 1.0
C16 A:JE4601 2.7 51.5 1.0
CL2 A:JE4601 3.1 66.3 1.0
CG A:GLN495 3.3 36.6 1.0
CD A:GLN495 3.7 53.9 1.0
CB A:GLN495 3.7 35.2 1.0
NE2 A:GLN495 4.0 43.6 1.0
C13 A:JE4601 4.0 52.3 1.0
C17 A:JE4601 4.0 51.4 1.0
CG A:GLN257 4.3 42.0 1.0
CB A:GLN257 4.3 39.6 1.0
OE1 A:GLN495 4.3 43.0 1.0
NH1 A:ARG111 4.4 56.2 1.0
O A:HOH866 4.4 55.9 1.0
C18 A:JE4601 4.5 51.5 1.0
CD A:ARG111 4.6 41.5 1.0
CZ A:ARG111 4.6 69.2 1.0
NE A:ARG111 4.6 51.5 1.0
OE1 A:GLN257 4.8 54.4 1.0
O A:HOH867 4.8 48.5 1.0
CD1 A:LEU254 5.0 31.8 1.0

Chlorine binding site 2 out of 4 in 6mdb

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Chlorine binding site 2 out of 4 in the Non-Receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor Pyrazolo-Pyrimidinone 5


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 Inhibitor Pyrazolo-Pyrimidinone 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl601

b:66.3
occ:1.00
 CL2 A:JE4601 0.0 66.3 1.0
C14 A:JE4601 1.7 56.5 1.0
C13 A:JE4601 2.7 52.3 1.0
C15 A:JE4601 2.7 57.3 1.0
C12 A:JE4601 3.0 49.2 1.0
CL1 A:JE4601 3.1 67.6 1.0
N6 A:JE4601 3.1 45.1 1.0
CG A:GLN257 3.3 42.0 1.0
CA A:LEU254 3.7 29.8 1.0
O A:THR253 3.7 36.6 1.0
CD A:ARG111 3.7 41.5 1.0
CB A:GLN257 3.8 39.6 1.0
CD1 A:LEU254 3.9 31.8 1.0
C18 A:JE4601 4.0 51.5 1.0
C16 A:JE4601 4.0 51.5 1.0
C1 A:JE4601 4.0 48.5 1.0
CG A:ARG111 4.1 41.0 1.0
NE A:ARG111 4.1 51.5 1.0
N5 A:JE4601 4.2 43.7 1.0
C A:THR253 4.3 36.1 1.0
N A:LEU254 4.3 31.9 1.0
CB A:LEU254 4.4 28.7 1.0
CD A:GLN257 4.5 59.9 1.0
C17 A:JE4601 4.5 51.4 1.0
O A:LEU254 4.6 32.1 1.0
C2 A:JE4601 4.6 46.2 1.0
C A:LEU254 4.7 33.7 1.0
CG A:LEU254 4.8 31.4 1.0
CZ A:ARG111 4.9 69.2 1.0
C4 A:JE4601 5.0 47.2 1.0
O1 A:JE4601 5.0 49.1 1.0

Chlorine binding site 3 out of 4 in 6mdb

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Chlorine binding site 3 out of 4 in the Non-Receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor Pyrazolo-Pyrimidinone 5


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 Inhibitor Pyrazolo-Pyrimidinone 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl601

b:66.1
occ:1.00
 CL1 B:JE4601 0.0 66.1 1.0
C15 B:JE4601 1.7 58.7 1.0
C14 B:JE4601 2.6 58.3 1.0
C16 B:JE4601 2.7 54.5 1.0
O B:HOH916 2.9 66.9 1.0
CL2 B:JE4601 3.0 69.4 1.0
CG B:GLN495 3.2 42.5 1.0
CD B:GLN495 3.4 53.7 1.0
NE2 B:GLN495 3.8 44.0 1.0
CB B:GLN495 3.8 33.2 1.0
OE1 B:GLN495 3.8 44.7 1.0
CG B:GLN257 3.9 56.1 1.0
CB B:GLN257 3.9 41.6 1.0
C13 B:JE4601 4.0 51.7 1.0
C17 B:JE4601 4.0 52.7 1.0
NH1 B:ARG111 4.3 59.5 1.0
CD B:ARG111 4.4 41.1 1.0
C18 B:JE4601 4.5 51.2 1.0
CZ B:ARG111 4.6 71.1 1.0
NE B:ARG111 4.6 51.0 1.0
CD1 B:LEU254 4.8 32.3 1.0
CD B:GLN257 4.9 71.5 1.0

Chlorine binding site 4 out of 4 in 6mdb

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Chlorine binding site 4 out of 4 in the Non-Receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor Pyrazolo-Pyrimidinone 5


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 Inhibitor Pyrazolo-Pyrimidinone 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl601

b:69.4
occ:1.00
 CL2 B:JE4601 0.0 69.4 1.0
C14 B:JE4601 1.7 58.3 1.0
C15 B:JE4601 2.7 58.7 1.0
C13 B:JE4601 2.7 51.7 1.0
CL1 B:JE4601 3.0 66.1 1.0
C12 B:JE4601 3.0 45.8 1.0
N6 B:JE4601 3.1 42.1 1.0
CG B:GLN257 3.3 56.1 1.0
CA B:LEU254 3.5 30.3 1.0
O B:THR253 3.5 34.9 1.0
CD B:ARG111 3.6 41.1 1.0
CB B:GLN257 3.9 41.6 1.0
CG B:ARG111 3.9 39.1 1.0
CD1 B:LEU254 4.0 32.3 1.0
C1 B:JE4601 4.0 46.1 1.0
C18 B:JE4601 4.0 51.2 1.0
C16 B:JE4601 4.0 54.5 1.0
N B:LEU254 4.0 31.7 1.0
C B:THR253 4.0 34.1 1.0
NE B:ARG111 4.1 51.0 1.0
N5 B:JE4601 4.2 43.1 1.0
O B:LEU254 4.3 36.4 1.0
CB B:LEU254 4.3 29.0 1.0
C B:LEU254 4.4 35.3 1.0
C17 B:JE4601 4.5 52.7 1.0
CD B:GLN257 4.5 71.5 1.0
C2 B:JE4601 4.6 45.6 1.0
NE2 B:GLN257 4.7 60.0 1.0
CG B:LEU254 4.7 32.2 1.0
O B:HOH720 4.9 43.7 1.0
CZ B:ARG111 4.9 71.1 1.0
O B:HOH916 4.9 66.9 1.0
CG2 B:THR253 4.9 36.5 1.0
C4 B:JE4601 4.9 44.7 1.0
OE1 B:GLN495 5.0 44.7 1.0

Reference:

P.Sarver, M.Acker, J.T.Bagdanoff, Z.Chen, Y.N.Chen, H.Chan, B.Firestone, M.Fodor, J.Fortanet, H.Hao, M.Hentemann, M.Kato, R.Koenig, L.R.Labonte, G.Liu, S.Liu, C.Liu, E.Mcneill, M.Mohseni, M.Sendzik, T.Stams, S.Spence, V.Tamez, R.Tichkule, C.Towler, H.Wang, P.Wang, S.L.Williams, B.Yu, M.J.Lamarche. 6-Amino-3-Methylpyrimidinones As Potent, Selective, and Orally Efficacious SHP2 Inhibitors. J. Med. Chem. V. 62 1793 2019.
ISSN: ISSN 1520-4804
PubMed: 30688459
DOI: 10.1021/ACS.JMEDCHEM.8B01726
Page generated: Sat Dec 12 13:21:02 2020

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