Fluorine in PDB 6md7: Non-Receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor Pyrimidinone 7

Enzymatic activity of Non-Receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor Pyrimidinone 7

All present enzymatic activity of Non-Receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor Pyrimidinone 7:
3.1.3.48;

Protein crystallography data

The structure of Non-Receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor Pyrimidinone 7, PDB code: 6md7 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) 19.59 / 1.96
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 46.050, 213.590, 55.910, 90.00, 96.51, 90.00
R / Rfree (%) 17 / 20.9

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Non-Receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor Pyrimidinone 7 (pdb code 6md7). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Non-Receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor Pyrimidinone 7, PDB code: 6md7:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 6md7

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Fluorine binding site 1 out of 6 in the Non-Receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor Pyrimidinone 7


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Non-Receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor Pyrimidinone 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:37.1
occ:1.00
 F1 A:JE1601 0.0 37.1 1.0
C17 A:JE1601 1.3 35.9 1.0
F2 A:JE1601 2.1 33.0 1.0
F3 A:JE1601 2.1 41.1 1.0
C16 A:JE1601 2.3 30.0 1.0
N5 A:JE1601 2.6 28.7 1.0
CG A:GLN495 3.0 17.2 1.0
O A:HOH983 3.2 58.9 1.0
CB A:GLN495 3.2 16.9 1.0
C12 A:JE1601 3.6 25.7 1.0
O A:HOH951 3.6 52.0 1.0
CD A:GLN495 3.8 30.9 1.0
C15 A:JE1601 3.9 23.7 1.0
O A:HOH764 4.1 28.7 1.0
NE2 A:GLN495 4.2 23.1 1.0
O A:HOH839 4.3 35.1 1.0
OE1 A:GLN495 4.4 31.7 1.0
S1 A:JE1601 4.5 25.6 1.0
C13 A:JE1601 4.7 24.1 1.0
CA A:GLN495 4.7 15.7 1.0
CG A:GLN257 4.7 27.4 1.0
O A:PRO491 4.7 22.1 1.0
C14 A:JE1601 4.8 24.7 1.0
CZ A:ARG111 4.8 54.2 1.0
CB A:GLN257 4.9 22.3 1.0
CA A:LYS492 4.9 18.7 1.0
NH1 A:ARG111 5.0 31.1 1.0

Fluorine binding site 2 out of 6 in 6md7

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Fluorine binding site 2 out of 6 in the Non-Receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor Pyrimidinone 7


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Non-Receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor Pyrimidinone 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:33.0
occ:1.00
 F2 A:JE1601 0.0 33.0 1.0
C17 A:JE1601 1.3 35.9 1.0
F1 A:JE1601 2.1 37.1 1.0
F3 A:JE1601 2.2 41.1 1.0
C16 A:JE1601 2.4 30.0 1.0
C12 A:JE1601 2.9 25.7 1.0
S1 A:JE1601 3.0 25.6 1.0
N5 A:JE1601 3.5 28.7 1.0
CG A:GLN257 3.5 27.4 1.0
CD1 A:LEU254 3.5 23.6 1.0
CB A:GLN257 3.8 22.3 1.0
CB A:GLN495 3.8 16.9 1.0
CG A:GLN495 3.9 17.2 1.0
CD A:GLN495 3.9 30.9 1.0
OE1 A:GLN495 4.1 31.7 1.0
C13 A:JE1601 4.3 24.1 1.0
CA A:LEU254 4.4 20.1 1.0
NE2 A:GLN495 4.5 23.1 1.0
O A:PRO491 4.5 22.1 1.0
CD A:GLN257 4.6 35.5 1.0
C15 A:JE1601 4.6 23.7 1.0
O A:HOH951 4.7 52.0 1.0
C2 A:JE1601 4.7 23.8 1.0
CG A:LEU254 4.7 23.7 1.0
CB A:LEU254 4.7 19.7 1.0
NE A:ARG111 4.8 40.1 1.0
O A:LEU254 4.8 21.1 1.0
OE1 A:GLN257 4.8 33.6 1.0
CD A:ARG111 4.9 26.3 1.0
C A:PRO491 5.0 23.1 1.0
C14 A:JE1601 5.0 24.7 1.0

Fluorine binding site 3 out of 6 in 6md7

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Fluorine binding site 3 out of 6 in the Non-Receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor Pyrimidinone 7


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Non-Receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor Pyrimidinone 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:41.1
occ:1.00
 F3 A:JE1601 0.0 41.1 1.0
C17 A:JE1601 1.3 35.9 1.0
F1 A:JE1601 2.1 37.1 1.0
F2 A:JE1601 2.2 33.0 1.0
C16 A:JE1601 2.4 30.0 1.0
O A:HOH951 3.1 52.0 1.0
NE A:ARG111 3.2 40.1 1.0
N5 A:JE1601 3.2 28.7 1.0
C12 A:JE1601 3.3 25.7 1.0
CG A:GLN257 3.3 27.4 1.0
CZ A:ARG111 3.3 54.2 1.0
CD A:ARG111 3.4 26.3 1.0
NH1 A:ARG111 3.5 31.1 1.0
OE1 A:GLN257 3.5 33.6 1.0
S1 A:JE1601 3.7 25.6 1.0
CD A:GLN257 3.7 35.5 1.0
NH2 A:ARG111 4.0 40.3 1.0
CB A:GLN257 4.1 22.3 1.0
C15 A:JE1601 4.5 23.7 1.0
CG A:ARG111 4.5 24.5 1.0
O A:HOH983 4.6 58.9 1.0
C13 A:JE1601 4.6 24.1 1.0
CG A:GLN495 4.7 17.2 1.0
NE2 A:GLN257 4.8 24.4 1.0
O1 A:JE1601 4.8 21.4 1.0
CD A:GLN495 4.8 30.9 1.0
O A:HOH839 4.9 35.1 1.0
NE2 A:GLN495 4.9 23.1 1.0

Fluorine binding site 4 out of 6 in 6md7

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Fluorine binding site 4 out of 6 in the Non-Receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor Pyrimidinone 7


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Non-Receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor Pyrimidinone 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:39.8
occ:1.00
 F1 B:JE1601 0.0 39.8 1.0
C17 B:JE1601 1.3 33.2 1.0
F2 B:JE1601 2.1 34.7 1.0
F3 B:JE1601 2.1 26.5 1.0
C16 B:JE1601 2.4 31.8 1.0
O B:HOH813 3.1 53.0 1.0
NE B:ARG111 3.2 36.4 1.0
N5 B:JE1601 3.2 32.2 1.0
C12 B:JE1601 3.2 27.4 1.0
CG B:GLN257 3.4 33.5 1.0
S1 B:JE1601 3.6 24.3 1.0
CZ B:ARG111 3.6 50.4 1.0
OE1 B:GLN257 3.6 35.9 1.0
NH1 B:ARG111 3.7 38.3 1.0
CD B:GLN257 3.8 40.0 1.0
CD B:ARG111 3.8 28.5 1.0
O B:HOH836 3.9 45.4 1.0
CB B:GLN257 4.1 23.9 1.0
O B:HOH842 4.3 42.6 1.0
C15 B:JE1601 4.4 28.3 1.0
CG B:ARG111 4.4 27.3 1.0
NH2 B:ARG111 4.5 39.9 1.0
C13 B:JE1601 4.5 28.3 1.0
O1 B:JE1601 4.8 18.6 1.0
CG B:GLN495 4.9 25.6 1.0
CD B:GLN495 4.9 37.5 1.0
NE2 B:GLN257 4.9 22.6 1.0
NE2 B:GLN495 5.0 28.3 1.0
C14 B:JE1601 5.0 27.3 1.0

Fluorine binding site 5 out of 6 in 6md7

Go back to Fluorine Binding Sites List in 6md7
Fluorine binding site 5 out of 6 in the Non-Receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor Pyrimidinone 7


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Non-Receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor Pyrimidinone 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:34.7
occ:1.00
 F2 B:JE1601 0.0 34.7 1.0
C17 B:JE1601 1.3 33.2 1.0
F3 B:JE1601 2.1 26.5 1.0
F1 B:JE1601 2.1 39.8 1.0
C16 B:JE1601 2.3 31.8 1.0
N5 B:JE1601 2.6 32.2 1.0
O B:HOH842 2.9 42.6 1.0
CG B:GLN495 3.1 25.6 1.0
CB B:GLN495 3.2 18.4 1.0
C12 B:JE1601 3.7 27.4 1.0
CD B:GLN495 3.7 37.5 1.0
O B:HOH813 3.7 53.0 1.0
C15 B:JE1601 3.9 28.3 1.0
O B:HOH909 4.2 32.8 1.0
NE2 B:GLN495 4.2 28.3 1.0
OE1 B:GLN495 4.2 33.0 1.0
O B:HOH858 4.5 38.0 1.0
S1 B:JE1601 4.5 24.3 1.0
O B:PRO491 4.7 20.8 1.0
CG B:GLN257 4.7 33.5 1.0
C13 B:JE1601 4.7 28.3 1.0
CA B:GLN495 4.8 17.2 1.0
CB B:GLN257 4.8 23.9 1.0
C14 B:JE1601 4.9 27.3 1.0
CD1 B:LEU254 4.9 22.5 1.0
CA B:LYS492 4.9 17.7 1.0

Fluorine binding site 6 out of 6 in 6md7

Go back to Fluorine Binding Sites List in 6md7
Fluorine binding site 6 out of 6 in the Non-Receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor Pyrimidinone 7


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Non-Receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor Pyrimidinone 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:26.5
occ:1.00
 F3 B:JE1601 0.0 26.5 1.0
C17 B:JE1601 1.3 33.2 1.0
F2 B:JE1601 2.1 34.7 1.0
F1 B:JE1601 2.1 39.8 1.0
C16 B:JE1601 2.4 31.8 1.0
S1 B:JE1601 3.0 24.3 1.0
C12 B:JE1601 3.0 27.4 1.0
CD1 B:LEU254 3.4 22.5 1.0
CG B:GLN257 3.5 33.5 1.0
N5 B:JE1601 3.5 32.2 1.0
CB B:GLN257 3.7 23.9 1.0
OE1 B:GLN495 3.9 33.0 1.0
CD B:GLN495 3.9 37.5 1.0
CB B:GLN495 4.0 18.4 1.0
CG B:GLN495 4.1 25.6 1.0
CA B:LEU254 4.3 20.8 1.0
C13 B:JE1601 4.4 28.3 1.0
NE2 B:GLN495 4.5 28.3 1.0
O B:LEU254 4.5 21.5 1.0
O B:HOH813 4.6 53.0 1.0
O B:PRO491 4.6 20.8 1.0
CD B:GLN257 4.6 40.0 1.0
CB B:LEU254 4.6 20.4 1.0
CG B:LEU254 4.6 23.2 1.0
C15 B:JE1601 4.7 28.3 1.0
C2 B:JE1601 4.8 24.4 1.0
OE1 B:GLN257 4.8 35.9 1.0
O B:HOH842 4.9 42.6 1.0
C B:LEU254 4.9 22.2 1.0
CB B:PRO491 5.0 22.5 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: Sun Dec 13 12:58:45 2020

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