Chlorine in PDB 4lyh: Crystal Structure of Small Molecule Vinylsulfonamide 9 Covalently Bound to K-Ras G12C

The structure of Crystal Structure of Small Molecule Vinylsulfonamide 9 Covalently Bound to K-Ras G12C, PDB code: 4lyh was solved by J.M.Ostrem, U.Peters, M.L.Sos, J.A.Wells, K.M.Shokat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.12 / 1.37
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	68.029, 83.525, 86.975, 90.00, 111.13, 90.00
R / Rfree (%)	16.5 / 18.8

The structure of Crystal Structure of Small Molecule Vinylsulfonamide 9 Covalently Bound to K-Ras G12C also contains other interesting chemical elements:

Iodine

(I)

2 atoms

The binding sites of Chlorine atom in the Crystal Structure of Small Molecule Vinylsulfonamide 9 Covalently Bound to K-Ras G12C (pdb code 4lyh). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of Small Molecule Vinylsulfonamide 9 Covalently Bound to K-Ras G12C, PDB code: 4lyh:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Crystal Structure of Small Molecule Vinylsulfonamide 9 Covalently Bound to K-Ras G12C


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Small Molecule Vinylsulfonamide 9 Covalently Bound to K-Ras G12C within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl201 b:20.0 occ:1.00 CL1 B:21F201 0.0 20.0 1.0 C02 B:21F201 1.7 16.0 1.0 C26 B:21F201 2.7 15.7 1.0 C03 B:21F201 2.7 18.3 1.0 H261 B:21F201 2.8 18.9 1.0 HB2 B:TYR71 2.9 23.3 1.0 HG3 B:MET72 3.2 21.3 1.0 HB3 B:ARG68 3.2 23.6 1.0 HA B:ARG68 3.2 22.4 1.0 HG11 B:VAL7 3.2 22.9 1.0 HD2 B:TYR71 3.4 29.3 1.0 I04 B:21F201 3.4 31.2 1.0 HG12 B:VAL9 3.5 17.4 1.0 O B:ARG68 3.6 17.7 1.0 HB3 B:TYR71 3.6 23.3 1.0 CB B:TYR71 3.6 19.4 1.0 HG2 B:ARG68 3.6 22.2 1.0 CB B:ARG68 3.8 19.7 1.0 CA B:ARG68 3.8 18.6 1.0 CG1 B:VAL7 3.9 19.1 1.0 HG2 B:MET72 3.9 21.3 1.0 CG B:MET72 4.0 17.8 1.0 C23 B:21F201 4.0 15.9 1.0 HG12 B:VAL7 4.0 22.9 1.0 C05 B:21F201 4.0 17.1 1.0 HG13 B:VAL7 4.0 22.9 1.0 HE2 B:MET72 4.1 28.2 1.0 HD2 B:ARG68 4.1 20.7 1.0 CD2 B:TYR71 4.1 24.4 1.0 HG21 B:THR58 4.1 29.5 1.0 C B:ARG68 4.2 19.3 1.0 CG B:ARG68 4.2 18.5 1.0 HG11 B:VAL9 4.2 17.4 1.0 H B:MET72 4.2 20.0 1.0 CG1 B:VAL9 4.3 14.5 1.0 CG B:TYR71 4.4 23.3 1.0 N B:MET72 4.4 16.7 1.0 C06 B:21F201 4.5 16.6 1.0 H252 B:21F201 4.6 22.6 1.0 HB2 B:ARG68 4.7 23.6 1.0 CD B:ARG68 4.7 17.3 1.0 HE1 B:PHE78 4.7 18.7 1.0 C B:TYR71 4.7 17.1 1.0 HA B:MET72 4.7 21.5 1.0 CA B:TYR71 4.8 18.1 1.0 H051 B:21F201 4.8 20.5 1.0 HG13 B:VAL9 4.8 17.4 1.0 CE B:MET72 4.9 23.5 1.0 SD B:MET72 4.9 19.9 1.0 H B:TYR71 5.0 22.8 1.0 CA B:MET72 5.0 17.9 1.0

Chlorine binding site 2 out of 2 in the Crystal Structure of Small Molecule Vinylsulfonamide 9 Covalently Bound to K-Ras G12C


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Small Molecule Vinylsulfonamide 9 Covalently Bound to K-Ras G12C within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl202 b:22.1 occ:0.39 CL1 C:21F202 0.0 22.1 0.4 C02 C:21F202 1.7 29.9 0.4 HB2 C:TYR71 2.5 35.9 1.0 C26 C:21F202 2.6 30.1 0.4 H261 C:21F202 2.7 36.2 0.4 C03 C:21F202 2.7 29.0 0.4 HG3 C:MET72 2.9 34.7 1.0 HB3 C:TYR71 3.1 35.9 1.0 HG11 C:VAL7 3.2 21.8 1.0 CB C:TYR71 3.2 29.9 1.0 HA C:ARG68 3.4 48.1 1.0 HG21 C:THR58 3.4 36.4 1.0 I04 C:21F202 3.5 32.7 0.4 HG2 C:MET72 3.6 34.7 1.0 CG C:MET72 3.7 28.9 1.0 H C:MET72 3.7 34.0 1.0 HD2 C:TYR71 3.8 55.9 1.0 O C:ARG68 3.8 33.5 1.0 N C:MET72 3.8 28.4 1.0 HG22 C:THR58 3.8 36.4 1.0 HE2 C:MET72 3.9 62.1 1.0 C23 C:21F202 3.9 26.7 0.4 C C:TYR71 4.0 27.6 1.0 HD23 C:LEU56 4.0 34.9 1.0 C05 C:21F202 4.0 31.6 0.4 CG1 C:VAL7 4.0 18.1 1.0 HG13 C:VAL7 4.1 21.8 1.0 CG2 C:THR58 4.1 30.3 1.0 HE3 C:MET72 4.1 62.1 1.0 CA C:TYR71 4.2 29.3 1.0 HA C:MET72 4.3 32.4 1.0 CG C:TYR71 4.3 41.2 1.0 CA C:ARG68 4.3 40.1 1.0 CD2 C:TYR71 4.4 46.5 1.0 CE C:MET72 4.4 51.8 1.0 HG2 C:ARG68 4.4 59.1 1.0 HE2 C:PHE78 4.4 19.9 1.0 HG12 C:VAL7 4.4 21.8 1.0 HG23 C:THR58 4.4 36.4 1.0 H C:TYR71 4.4 38.1 1.0 HD21 C:LEU56 4.4 34.9 1.0 C06 C:21F202 4.5 29.9 0.4 C C:ARG68 4.5 36.4 1.0 CA C:MET72 4.5 27.0 1.0 O C:TYR71 4.5 25.8 1.0 H253 C:21F202 4.5 38.5 0.4 HG21 C:VAL7 4.6 21.2 1.0 HG12 C:VAL9 4.6 21.4 1.0 CD2 C:LEU56 4.7 29.1 1.0 CB C:MET72 4.7 28.3 1.0 N C:TYR71 4.7 31.7 1.0 HG11 C:VAL9 4.8 21.4 1.0 O C:MET67 4.8 37.7 1.0 H051 C:21F202 4.8 37.9 0.4 SD C:MET72 4.9 30.9 1.0 HA C:TYR71 5.0 35.2 1.0 HB2 C:MET72 5.0 34.0 1.0

J.M.Ostrem, U.Peters, M.L.Sos, J.A.Wells, K.M.Shokat. K-Ras(G12C) Inhibitors Allosterically Control Gtp Affinity and Effector Interactions. Nature V. 503 548 2013.
ISSN: ISSN 0028-0836
PubMed: 24256730
DOI: 10.1038/NATURE12796