Chlorine in PDB 6d5h: 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: 6d5h 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)	43.34 / 1.80
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	184.142, 184.142, 179.238, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 18.9

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 6d5h). 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: 6d5h:
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:68.3 occ:1.00 O A:HOH371 3.2 48.6 1.0 N A:ARG41 3.3 18.3 1.0 ND2 B:ASN976 3.5 17.1 1.0 O B:HOH2368 3.7 29.1 1.0 O A:ARG41 3.7 18.4 1.0 CA A:TYR40 3.9 18.3 1.0 O A:HOH316 4.0 32.3 1.0 C A:TYR40 4.1 18.3 1.0 CB A:TYR40 4.2 18.3 1.0 CA A:ARG41 4.3 18.3 1.0 CD2 A:TYR40 4.3 21.9 1.0 O B:HOH2426 4.3 43.9 1.0 C A:ARG41 4.5 18.4 1.0 CG B:ASN976 4.5 15.9 1.0 CB A:ARG41 4.6 18.4 1.0 CG2 A:ILE24 4.7 18.5 1.0 O A:HOH352 4.7 16.3 1.0 CG A:TYR40 4.7 18.3 1.0 OD1 B:ASN976 4.8 19.7 1.0 O A:SER39 4.8 18.4 0.3 CA B:GLN973 4.9 15.5 1.0 O A:SER39 4.9 18.4 0.7

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:25.4 occ:1.00 CL B:FV72001 0.0 25.4 1.0 C9 B:FV72001 1.7 21.8 1.0 C10 B:FV72001 2.7 17.8 1.0 C8 B:FV72001 2.7 25.3 1.0 ND2 B:ASN879 3.4 30.9 1.0 CD1 B:LEU901 3.7 17.1 1.0 CG B:LEU901 3.7 16.9 1.0 OD1 B:ASN879 3.7 26.8 1.0 CG B:ASN879 3.8 26.0 1.0 CB B:HIS905 3.8 20.9 1.0 C11 B:FV72001 3.9 19.3 1.0 CG1 B:VAL875 4.0 16.1 1.0 CB B:MET878 4.0 15.4 1.0 C7 B:FV72001 4.0 27.9 1.0 CD2 B:LEU901 4.1 17.3 1.0 O B:VAL875 4.1 15.5 1.0 ND1 B:HIS905 4.2 37.4 1.0 CG B:HIS905 4.3 31.4 1.0 C6 B:FV72001 4.5 22.0 1.0 CA B:VAL875 4.5 16.8 1.0 O B:LEU901 4.5 17.8 1.0 CB B:VAL875 4.6 15.3 1.0 O B:HOH2413 4.7 34.4 1.0 N B:ASN879 4.7 15.6 1.0 C B:MET878 4.7 15.7 1.0 CG2 B:VAL875 4.8 15.2 1.0 CA B:HIS905 4.8 17.4 1.0 C B:VAL875 4.8 16.0 1.0 CB B:ASN879 4.9 15.8 1.0 CG B:MET878 4.9 15.3 1.0 CA B:MET878 5.0 15.4 1.0 O B:HOH2106 5.0 39.7 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:Cl2001 b:97.6 occ:1.00 CL1 B:FV72001 0.0 97.6 1.0 C17 B:FV72001 1.7 39.2 1.0 C16 B:FV72001 2.6 45.5 1.0 C12 B:FV72001 2.7 36.3 1.0 C7 B:FV72001 3.1 27.9 1.0 C6 B:FV72001 3.4 22.0 1.0 N1 B:FV72001 3.6 21.9 1.0 CE1 B:PHE890 3.8 19.0 1.0 O B:LYS898 3.8 20.7 1.0 C8 B:FV72001 3.9 25.3 1.0 C15 B:FV72001 3.9 40.7 1.0 C13 B:FV72001 4.0 42.8 1.0 CB B:LYS898 4.1 17.8 1.0 CA B:LYS898 4.2 17.0 1.0 C11 B:FV72001 4.3 19.3 1.0 C24 B:FV72001 4.3 19.2 1.0 CG B:LYS898 4.4 20.0 1.0 C B:LYS898 4.4 19.0 1.0 CD2 B:LEU901 4.4 17.3 1.0 C14 B:FV72001 4.4 43.5 1.0 O B:HOH2386 4.5 36.8 1.0 CD1 B:PHE890 4.5 20.3 1.0 C5 B:FV72001 4.5 19.2 1.0 C22 B:FV72001 4.6 19.0 1.0 CB B:LEU901 4.6 19.1 1.0 CZ B:PHE890 4.7 21.2 1.0 N B:GLU902 4.7 16.7 1.0 O B:HOH2829 4.7 46.5 1.0 CG B:LEU901 4.7 16.9 1.0 C9 B:FV72001 4.7 21.8 1.0 O B:HOH2564 4.8 39.8 1.0 CB B:GLU902 4.9 28.1 1.0 O B:HOH2824 4.9 40.0 1.0 N B:FV72001 4.9 17.0 1.0 C10 B:FV72001 5.0 17.8 1.0 CA B:GLU902 5.0 18.9 1.0 C23 B:FV72001 5.0 17.5 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:49.3 occ:1.00 O C:HOH469 2.4 54.5 1.0 O C:HOH468 2.9 41.3 1.0 N C:THR87 3.0 17.7 0.8 N C:THR87 3.0 17.7 0.2 O C:HOH418 3.3 21.8 1.0 OG1 C:THR87 3.3 18.2 0.2 OG1 C:THR124 3.3 21.5 1.0 O C:ASN85 3.3 21.4 1.0 CA C:ASN86 3.5 17.2 1.0 OG1 C:THR87 3.5 22.4 0.8 C C:ASN86 3.7 17.5 1.0 CB C:THR87 3.9 19.6 0.8 CG2 C:THR87 3.9 19.9 0.2 CG2 C:THR124 3.9 25.2 1.0 C C:ASN85 3.9 21.8 1.0 CB C:THR87 3.9 20.1 0.2 CB C:THR124 4.0 21.8 1.0 CA C:THR87 4.0 17.9 0.8 N C:ASN86 4.0 17.0 1.0 CA C:THR87 4.1 17.9 0.2 O C:HOH423 4.5 37.1 1.0 CB C:ASN86 4.6 18.1 1.0 CG C:ASN86 4.8 19.8 1.0 N C:LYS88 4.9 18.1 0.8 ND2 C:ASN86 4.9 19.6 1.0 N C:LYS88 4.9 18.6 0.2 O C:ASN86 5.0 17.5 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:77.9 occ:1.00 N C:ASP47 3.3 33.7 1.0 O C:VAL45 3.8 34.3 1.0 NH2 C:ARG161 3.8 26.9 1.0 CA C:ILE46 3.9 34.0 1.0 OD1 C:ASP47 4.0 35.4 1.0 C C:ILE46 4.1 33.9 1.0 CA C:ASP47 4.1 33.6 1.0 CE2 C:TYR157 4.3 34.8 1.0 CD2 C:TYR157 4.3 32.7 1.0 C C:VAL45 4.6 34.5 1.0 CG2 C:ILE46 4.7 33.5 1.0 N C:ILE46 4.7 34.4 1.0 CG C:ASP47 4.9 33.7 1.0 CB C:ILE46 4.9 33.9 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