Atomistry » Fluorine » PDB 6lub-6mii » 6md7
Atomistry »
  Fluorine »
    PDB 6lub-6mii »
      6md7 »

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

Go back to Fluorine Binding Sites List in 6md7
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

Go back to Fluorine Binding Sites List in 6md7
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

Go back to Fluorine Binding Sites List in 6md7
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

Go back to Fluorine Binding Sites List in 6md7
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: Tue Jul 15 13:08:11 2025

Last articles

Mg in 7AF5
Mg in 7AFD
Mg in 7AF8
Mg in 7AF3
Mg in 7AFA
Mg in 7AE3
Mg in 7AE1
Mg in 7AEA
Mg in 7A4P
Mg in 7ADT
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy