Chlorine in PDB 6d5l: Ras:Sos:Ras in Complex with A Small Molecule Activator

The structure of Ras:Sos:Ras in Complex with A Small Molecule Activator, PDB code: 6d5l was solved by J.Phan, T.Hodges, S.W.Fesik, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.69 / 1.70
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	183.757, 183.757, 178.445, 90.00, 90.00, 90.00
R / Rfree (%)	15.9 / 17.5

The structure of Ras:Sos:Ras in Complex with A Small Molecule Activator also contains other interesting chemical elements:

Fluorine	(F)	1 atom
Magnesium	(Mg)	1 atom
Sodium	(Na)	1 atom

The binding sites of Chlorine atom in the Ras:Sos:Ras in Complex with A Small Molecule Activator (pdb code 6d5l). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Ras:Sos:Ras in Complex with A Small Molecule Activator, PDB code: 6d5l:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Ras:Sos:Ras in Complex with A Small Molecule Activator


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Ras:Sos:Ras in Complex with A Small Molecule Activator within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl2001 b:19.6 occ:1.00 CL14 B:FW72001 0.0 19.6 1.0 C13 B:FW72001 1.7 17.2 1.0 C15 B:FW72001 2.6 16.4 1.0 C12 B:FW72001 2.7 19.4 1.0 ND2 B:ASN879 3.5 26.3 1.0 CD1 B:LEU901 3.7 15.8 1.0 CG B:LEU901 3.7 14.8 1.0 OD1 B:ASN879 3.7 24.1 1.0 CG B:ASN879 3.8 22.1 1.0 CB B:HIS905 3.8 15.4 1.0 CB B:MET878 3.9 9.9 1.0 C16 B:FW72001 3.9 14.8 1.0 CG1 B:VAL875 3.9 16.5 1.0 C11 B:FW72001 4.0 20.5 1.0 O B:VAL875 4.1 11.9 1.0 CD2 B:LEU901 4.1 12.9 1.0 CG B:HIS905 4.2 22.2 1.0 CA B:VAL875 4.4 10.7 1.0 O B:LEU901 4.4 14.2 1.0 ND1 B:HIS905 4.4 29.5 1.0 C10 B:FW72001 4.5 17.2 1.0 CB B:VAL875 4.5 13.8 1.0 O B:HOH2301 4.6 37.1 1.0 C B:MET878 4.6 12.9 1.0 CG2 B:VAL875 4.6 13.6 1.0 N B:ASN879 4.7 10.8 1.0 C B:VAL875 4.7 12.0 1.0 CA B:HIS905 4.7 13.9 1.0 CG B:MET878 4.8 11.8 1.0 CA B:MET878 4.9 10.3 1.0 CB B:ASN879 4.9 13.2 1.0 O B:MET878 5.0 13.3 1.0

Chlorine binding site 2 out of 2 in the Ras:Sos:Ras in Complex with A Small Molecule Activator


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Ras:Sos:Ras in Complex with A Small Molecule Activator within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl2001 b:53.0 occ:1.00 CL25 B:FW72001 0.0 53.0 1.0 C24 B:FW72001 1.7 22.8 1.0 C23 B:FW72001 2.7 19.0 1.0 C2 B:FW72001 2.7 21.7 1.0 F1 B:FW72001 2.9 20.9 1.0 CD2 B:LEU901 3.5 12.9 1.0 CE B:MET878 3.7 18.9 1.0 CD1 B:PHE890 3.8 19.5 1.0 CG1 B:ILE893 3.8 14.1 1.0 CG1 B:VAL852 3.9 13.5 1.0 C3 B:FW72001 3.9 15.1 1.0 C5 B:FW72001 4.0 14.4 1.0 CD1 B:ILE856 4.1 15.6 1.0 C4 B:FW72001 4.5 13.8 1.0 CB B:ILE893 4.5 14.4 1.0 CE1 B:PHE890 4.5 22.1 1.0 CG2 B:ILE893 4.5 18.5 1.0 CA B:PHE890 4.6 16.1 1.0 CD1 B:ILE893 4.7 22.8 1.0 CG B:PHE890 4.7 17.5 1.0 CB B:PHE890 4.8 14.6 1.0 CG B:LEU901 4.9 14.8 1.0

T.R.Hodges, J.R.Abbott, A.J.Little, D.Sarkar, J.M.Salovich, J.E.Howes, D.T.Akan, J.Sai, A.L.Arnold, C.Browning, M.C.Burns, T.Sobolik, Q.Sun, Y.Beesetty, J.A.Coker, D.Scharn, H.Stadtmueller, O.W.Rossanese, J.Phan, A.G.Waterson, D.B.Mcconnell, S.W.Fesik. Discovery and Structure-Based Optimization of Benzimidazole-Derived Activators of SOS1-Mediated Nucleotide Exchange on Ras. J. Med. Chem. V. 61 8875 2018.
ISSN: ISSN 1520-4804
PubMed: 30205005
DOI: 10.1021/ACS.JMEDCHEM.8B01108