Chlorine in PDB 6d5g: 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: 6d5g 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)	48.84 / 1.92
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	183.050, 183.050, 178.784, 90.00, 90.00, 90.00
R / Rfree (%)	15.5 / 17.3

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

The binding sites of Chlorine atom in the Ras:Sos:Ras in Complex with A Small Molecule Activator (pdb code 6d5g). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Ras:Sos:Ras in Complex with A Small Molecule Activator, PDB code: 6d5g:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 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 A:Cl204 b:59.9 occ:1.00 O A:HOH385 3.2 47.3 1.0 N A:ARG41 3.3 16.8 1.0 ND2 B:ASN976 3.4 12.7 1.0 O B:HOH2459 3.7 29.8 1.0 O A:ARG41 3.7 17.6 1.0 CA A:TYR40 3.9 17.6 1.0 O A:HOH320 4.0 35.1 1.0 C A:TYR40 4.1 18.6 1.0 CB A:TYR40 4.2 19.7 1.0 O B:HOH2409 4.3 47.6 1.0 CA A:ARG41 4.3 15.9 1.0 CD2 A:TYR40 4.3 21.5 1.0 C A:ARG41 4.4 15.6 1.0 CG B:ASN976 4.5 12.4 1.0 CB A:ARG41 4.6 19.1 1.0 O A:HOH337 4.7 17.0 1.0 CG2 A:ILE24 4.7 16.6 1.0 CG A:TYR40 4.7 16.6 1.0 OD1 B:ASN976 4.8 19.9 1.0 CA B:GLN973 4.8 12.0 1.0 O A:SER39 4.9 18.0 0.3 O A:SER39 5.0 15.8 0.7

Chlorine binding site 2 out of 4 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:28.1 occ:1.00 CL1 B:FVD2001 0.0 28.1 1.0 C19 B:FVD2001 1.7 27.6 1.0 C18 B:FVD2001 2.7 25.8 1.0 C20 B:FVD2001 2.7 18.6 1.0 CD1 B:LEU901 3.8 14.9 1.0 CD2 B:HIS905 3.8 19.2 1.0 CG B:LEU901 3.8 15.0 1.0 O B:VAL875 3.9 13.9 1.0 CG1 B:VAL875 4.0 13.7 1.0 CB B:HIS905 4.0 16.7 1.0 C21 B:FVD2001 4.0 19.2 1.0 C12 B:FVD2001 4.0 30.7 1.0 CD2 B:LEU901 4.0 16.9 1.0 CB B:MET878 4.0 11.8 1.0 CG B:ASN879 4.1 27.0 1.0 CG B:HIS905 4.1 20.3 1.0 OD1 B:ASN879 4.2 29.0 1.0 CB B:ASN879 4.3 16.7 1.0 N B:ASN879 4.3 14.3 1.0 C B:MET878 4.4 14.1 1.0 CA B:VAL875 4.4 14.1 1.0 C11 B:FVD2001 4.5 23.9 1.0 ND2 B:ASN879 4.5 27.8 1.0 C B:VAL875 4.6 13.3 1.0 CA B:ASN879 4.6 13.7 1.0 CB B:VAL875 4.6 13.9 1.0 O B:LEU901 4.7 15.1 1.0 O B:MET878 4.8 15.9 1.0 CA B:MET878 4.8 11.8 1.0 NE2 B:HIS905 4.9 25.7 1.0 CG2 B:VAL875 4.9 16.7 1.0

Chlorine binding site 3 out of 4 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 3 of Ras:Sos:Ras in Complex with A Small Molecule Activator within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl201 b:67.4 occ:1.00 N C:ASP47 3.2 29.1 1.0 O C:VAL45 3.6 30.0 1.0 CA C:ILE46 3.7 28.5 1.0 NH2 C:ARG161 3.9 25.1 1.0 C C:ILE46 3.9 29.6 1.0 OD1 C:ASP47 4.1 33.8 1.0 CA C:ASP47 4.1 30.7 1.0 CE2 C:TYR157 4.2 35.5 1.0 CD2 C:TYR157 4.2 33.1 1.0 C C:VAL45 4.5 30.2 1.0 N C:ILE46 4.5 28.8 1.0 CG2 C:ILE46 4.7 28.1 1.0 CB C:ILE46 4.7 28.4 1.0 O C:HOH370 4.8 50.7 1.0 CG C:ASP47 4.8 32.7 1.0 N C:GLY48 4.9 39.1 1.0

Chlorine binding site 4 out of 4 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 4 of Ras:Sos:Ras in Complex with A Small Molecule Activator within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl202 b:44.9 occ:1.00 O C:HOH462 2.2 46.2 1.0 N C:THR87 2.9 15.2 0.8 N C:THR87 2.9 16.8 0.2 O C:HOH457 3.0 42.4 1.0 OG1 C:THR87 3.1 19.8 0.2 O C:HOH397 3.2 21.3 1.0 OG1 C:THR124 3.3 18.6 1.0 OG1 C:THR87 3.4 22.1 0.8 O C:ASN85 3.5 18.4 1.0 CA C:ASN86 3.5 15.3 1.0 C C:ASN86 3.7 16.8 1.0 CB C:THR87 3.7 21.0 0.8 CG2 C:THR87 3.8 22.9 0.2 CB C:THR87 3.8 21.4 0.2 CG2 C:THR124 3.9 21.0 1.0 CB C:THR124 3.9 19.0 1.0 CA C:THR87 3.9 16.5 0.8 CA C:THR87 4.0 17.6 0.2 C C:ASN85 4.0 19.0 1.0 N C:ASN86 4.1 16.4 1.0 O C:HOH392 4.4 45.7 1.0 O C:HOH422 4.6 33.7 1.0 CB C:ASN86 4.7 15.5 1.0 N C:LYS88 4.8 16.0 1.0 CG C:ASN86 4.9 17.9 1.0 O C:ASN86 4.9 15.9 1.0 ND2 C:ASN86 4.9 18.2 1.0 C C:THR87 5.0 15.1 0.8 C C:THR87 5.0 15.6 0.2

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