Sodium in PDB 6v9j: Expanding the Chemical Landscape of SOS1 Activators Using Fragment Based Methods

The structure of Expanding the Chemical Landscape of SOS1 Activators Using Fragment Based Methods, PDB code: 6v9j was solved by J.Phan, S.W.Fesik, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.27 / 1.76
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	183.430, 183.430, 178.449, 90.00, 90.00, 90.00
R / Rfree (%)	15.6 / 16.6

The structure of Expanding the Chemical Landscape of SOS1 Activators Using Fragment Based Methods also contains other interesting chemical elements:

Fluorine	(F)	1 atom
Magnesium	(Mg)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the Expanding the Chemical Landscape of SOS1 Activators Using Fragment Based Methods (pdb code 6v9j). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Expanding the Chemical Landscape of SOS1 Activators Using Fragment Based Methods, PDB code: 6v9j:

Sodium binding site 1 out of 1 in the Expanding the Chemical Landscape of SOS1 Activators Using Fragment Based Methods


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Expanding the Chemical Landscape of SOS1 Activators Using Fragment Based Methods within 5.0Å range: probe atom residue distance (Å) B Occ C:Na202 b:34.2 occ:1.00 O C:HOH469 2.2 46.3 1.0 O C:HOH463 2.7 50.3 1.0 N C:THR87 2.9 14.9 0.7 N C:THR87 2.9 15.2 0.3 OG1 C:THR124 3.2 21.0 1.0 OG1 C:THR87 3.2 19.0 0.3 OG1 C:THR87 3.3 23.9 0.7 O C:HOH417 3.4 21.6 1.0 O C:ASN85 3.4 19.8 1.0 CA C:ASN86 3.5 12.7 1.0 CG2 C:THR87 3.6 22.0 0.3 CG2 C:THR124 3.7 22.8 1.0 CB C:THR87 3.7 19.6 0.7 C C:ASN86 3.7 13.9 1.0 CB C:THR124 3.7 19.6 1.0 CB C:THR87 3.8 19.6 0.3 CA C:THR87 3.9 16.4 0.7 CA C:THR87 3.9 16.4 0.3 C C:ASN85 3.9 20.0 1.0 N C:ASN86 4.0 16.3 1.0 O C:HOH342 4.6 55.5 1.0 O C:HOH443 4.7 41.1 1.0 CB C:ASN86 4.8 16.6 1.0 N C:LYS88 4.9 17.1 1.0 O C:ASN86 4.9 15.3 1.0 C C:THR87 5.0 15.3 0.7 C C:THR87 5.0 15.9 0.3 CG C:ASN86 5.0 19.1 1.0

D.Sarkar, E.T.Olejniczak, J.Phan, J.A.Coker, J.Sai, A.Arnold, Y.Beesetty, A.G.Waterson, S.W.Fesik. Discovery of Sulfonamide-Derived Agonists of SOS1-Mediated Nucleotide Exchange on Ras Using Fragment-Based Methods. J.Med.Chem. V. 63 8325 2020.
ISSN: ISSN 0022-2623
PubMed: 32673492
DOI: 10.1021/ACS.JMEDCHEM.0C00511