Chlorine in PDB 6d5e: 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: 6d5e 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)	48.73 / 1.75
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	183.613, 183.613, 179.178, 90.00, 90.00, 90.00
R / Rfree (%)	16 / 17.4

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 6d5e). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Ras:Sos:Ras in Complex with A Small Molecule Activator, PDB code: 6d5e:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 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:Cl203 b:59.4 occ:1.00 O A:HOH369 3.1 47.3 1.0 N A:ARG41 3.3 18.3 1.0 ND2 B:ASN976 3.4 21.1 1.0 O A:ARG41 3.7 18.4 1.0 O B:HOH2432 3.7 36.9 1.0 CA A:TYR40 3.8 21.1 1.0 C A:TYR40 4.0 19.9 1.0 CB A:TYR40 4.1 21.9 1.0 O A:HOH304 4.2 44.0 1.0 CD2 A:TYR40 4.2 25.9 1.0 CA A:ARG41 4.3 17.3 1.0 C A:ARG41 4.4 18.7 1.0 CG B:ASN976 4.5 17.7 1.0 CG2 A:ILE24 4.6 17.9 1.0 CB A:ARG41 4.6 24.8 1.0 CG A:TYR40 4.6 20.4 1.0 O A:HOH453 4.7 58.1 1.0 O A:HOH348 4.7 18.4 1.0 OD1 B:ASN976 4.8 22.8 1.0 O A:SER39 4.8 20.4 0.4 O A:SER39 4.8 21.7 0.6 CA B:GLN973 4.9 14.9 1.0

Chlorine binding site 2 out of 5 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:27.9 occ:1.00 CL B:FVG2001 0.0 27.9 1.0 C9 B:FVG2001 1.8 25.0 1.0 C10 B:FVG2001 2.7 19.3 1.0 C8 B:FVG2001 2.7 23.6 1.0 CD2 B:HIS905 3.8 23.8 1.0 CB B:HIS905 3.9 17.7 1.0 CD1 B:LEU901 3.9 18.4 1.0 OD1 B:ASN879 3.9 33.4 1.0 C11 B:FVG2001 3.9 18.4 1.0 CG B:LEU901 4.0 17.8 1.0 O B:VAL875 4.0 17.4 1.0 CG1 B:VAL875 4.0 19.0 1.0 CG B:ASN879 4.0 30.5 1.0 CG B:HIS905 4.0 23.0 1.0 C7 B:FVG2001 4.1 26.7 1.0 CB B:MET878 4.2 15.3 1.0 CD2 B:LEU901 4.2 19.4 1.0 CB B:ASN879 4.2 21.1 1.0 N B:ASN879 4.3 17.7 1.0 C B:MET878 4.5 17.1 1.0 C6 B:FVG2001 4.5 21.1 1.0 ND2 B:ASN879 4.5 29.9 1.0 CA B:VAL875 4.6 15.8 1.0 CA B:ASN879 4.6 18.1 1.0 C B:VAL875 4.7 16.3 1.0 CB B:VAL875 4.7 20.1 1.0 O B:LEU901 4.8 17.6 1.0 O B:MET878 4.8 20.3 1.0 NE2 B:HIS905 4.9 27.2 1.0 CA B:MET878 4.9 14.3 1.0 CG2 B:VAL875 5.0 21.4 1.0 CA B:HIS905 5.0 18.0 1.0

Chlorine binding site 3 out of 5 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 B:Cl2010 b:54.9 occ:1.00 O B:HOH2648 2.3 57.3 1.0 O B:HOH2491 3.2 32.1 1.0 NZ B:LYS837 3.2 31.6 1.0 CA B:PRO996 3.7 19.4 1.0 CD1 B:TRP834 3.8 21.3 1.0 CE B:LYS837 3.9 29.3 1.0 O B:HOH2382 4.0 46.3 1.0 O B:HOH2625 4.1 40.0 1.0 CD B:LYS837 4.1 19.3 1.0 NE1 B:TRP834 4.1 21.6 1.0 N B:PRO996 4.2 20.1 1.0 CB B:PRO996 4.3 18.9 1.0 O B:HOH2762 4.4 37.0 1.0 O B:HOH2292 4.4 32.7 1.0 O B:ASN995 4.4 21.1 1.0 C B:ASN995 4.4 20.2 1.0 O B:HOH2779 4.6 36.4 1.0 O B:PRO996 4.7 22.1 1.0 C B:PRO996 4.7 20.3 1.0 CD B:PRO996 4.9 19.4 1.0

Chlorine binding site 4 out of 5 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:Cl201 b:69.1 occ:1.00 N C:ASP47 3.2 34.0 1.0 O C:VAL45 3.7 36.7 1.0 NH2 C:ARG161 3.8 30.8 1.0 CA C:ILE46 3.8 31.0 1.0 C C:ILE46 4.0 34.7 1.0 OD1 C:ASP47 4.1 46.1 1.0 CA C:ASP47 4.2 33.4 1.0 CE2 C:TYR157 4.2 37.7 1.0 CD2 C:TYR157 4.2 35.3 1.0 C C:VAL45 4.5 36.1 1.0 N C:ILE46 4.6 32.3 1.0 CG2 C:ILE46 4.7 35.4 1.0 CB C:ILE46 4.8 30.8 1.0 CG C:ASP47 4.9 37.3 1.0

Chlorine binding site 5 out of 5 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 5 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:57.5 occ:1.00 O C:HOH1010 2.3 55.0 1.0 O B:HOH2128 2.4 39.5 1.0 N C:ASP57 2.8 18.5 1.0 O C:ILE55 3.2 22.6 1.0 NZ B:LYS939 3.3 25.9 1.0 O C:ASP57 3.4 22.5 1.0 CA C:LEU56 3.5 16.7 1.0 C C:LEU56 3.7 19.6 1.0 CA C:ASP57 3.8 17.2 1.0 C C:ASP57 3.9 19.3 1.0 CE1 B:HIS911 3.9 31.8 1.0 ND1 B:HIS911 3.9 29.9 1.0 C C:ILE55 4.1 22.0 1.0 CD1 C:LEU56 4.1 26.5 1.0 CB C:ASP57 4.1 20.2 1.0 CB C:TYR40 4.2 49.1 1.0 N C:LEU56 4.3 17.5 1.0 O B:HOH2557 4.4 42.4 1.0 CB C:LEU56 4.6 18.7 1.0 CG C:TYR40 4.7 44.9 1.0 CE B:LYS939 4.7 24.6 1.0 O C:HOH1006 4.7 33.3 1.0 CG C:LEU56 4.8 21.9 1.0 CD2 C:TYR40 4.8 50.4 1.0 O C:LEU56 4.9 20.0 1.0 N C:THR58 4.9 19.6 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