Iodine 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:

Chlorine

(Cl)

2 atoms

The binding sites of Iodine 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 Iodine atom.
In total 2 binding sites of Iodine where determined in the Crystal Structure of Small Molecule Vinylsulfonamide 9 Covalently Bound to K-Ras G12C, PDB code: 4lyh:
Jump to Iodine binding site number: 1; 2;

Iodine 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 Iodine with other atoms in the I 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:I201 b:31.2 occ:1.00 I04 B:21F201 0.0 31.2 1.0 C03 B:21F201 2.0 18.3 1.0 O B:HOH312 2.1 26.3 1.0 C05 B:21F201 2.9 17.1 1.0 H051 B:21F201 3.0 20.5 1.0 C02 B:21F201 3.1 16.0 1.0 HG21 B:THR58 3.1 29.5 1.0 HB3 B:GLU62 3.4 33.9 1.0 HB B:THR58 3.4 32.5 1.0 CL1 B:21F201 3.4 20.0 1.0 OG1 B:THR58 3.5 29.4 1.0 O B:HOH357 3.7 27.6 1.0 HG2 B:ARG68 3.7 22.2 1.0 HB2 B:GLU62 3.8 33.9 1.0 CB B:THR58 3.8 27.1 1.0 HG1 B:THR58 3.8 35.3 1.0 CG2 B:THR58 3.9 24.6 1.0 CB B:GLU62 4.0 28.2 1.0 HA B:GLU62 4.0 30.9 1.0 HG12 B:VAL9 4.1 17.4 1.0 O B:VAL8 4.1 14.7 1.0 HD2 B:TYR71 4.2 29.3 1.0 C06 B:21F201 4.2 16.6 1.0 HA B:VAL9 4.3 13.9 1.0 C26 B:21F201 4.3 15.7 1.0 HD2 B:ARG68 4.4 20.7 1.0 HE3 B:LYS16 4.4 16.5 1.0 HG22 B:THR58 4.4 29.5 1.0 HG23 B:THR58 4.5 29.5 1.0 HD3 B:ARG68 4.6 20.7 1.0 HG13 B:VAL7 4.6 22.9 1.0 CA B:GLU62 4.6 25.7 1.0 CG B:ARG68 4.6 18.5 1.0 HG12 B:VAL7 4.7 22.9 1.0 CD B:ARG68 4.8 17.3 1.0 C23 B:21F201 4.8 15.9 1.0 CD2 B:TYR71 4.8 24.4 1.0 HG11 B:VAL7 4.9 22.9 1.0 CG1 B:VAL7 4.9 19.1 1.0 HA B:ARG68 5.0 22.4 1.0 H082 B:21F201 5.0 19.1 1.0

Iodine 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 Iodine with other atoms in the I 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:I202 b:32.7 occ:0.39 I04 C:21F202 0.0 32.7 0.4 C03 C:21F202 2.1 29.0 0.4 HD2 C:TYR71 2.6 55.9 1.0 HG22 C:THR58 2.8 36.4 1.0 C05 C:21F202 3.0 31.6 0.4 H051 C:21F202 3.0 37.9 0.4 C02 C:21F202 3.1 29.9 0.4 CD2 C:TYR71 3.4 46.5 1.0 HD21 C:LEU56 3.4 34.9 1.0 CL1 C:21F202 3.5 22.1 0.4 CG2 C:THR58 3.6 30.3 1.0 HG21 C:THR58 3.6 36.4 1.0 HE2 C:TYR71 3.7 61.4 1.0 HB C:THR58 3.8 39.2 1.0 HA C:ARG68 3.9 48.1 1.0 HB2 C:TYR71 3.9 35.9 1.0 O C:HOH373 3.9 36.7 1.0 CE2 C:TYR71 3.9 51.1 1.0 O C:HOH374 4.1 44.2 1.0 CB C:THR58 4.3 32.7 1.0 CD2 C:LEU56 4.3 29.1 1.0 HD23 C:LEU56 4.3 34.9 1.0 HA C:THR58 4.3 40.4 1.0 HG23 C:THR58 4.3 36.4 1.0 C06 C:21F202 4.3 29.9 0.4 CG C:TYR71 4.4 41.2 1.0 C26 C:21F202 4.4 30.1 0.4 CB C:TYR71 4.5 29.9 1.0 O C:MET67 4.6 37.7 1.0 HG2 C:ARG68 4.7 59.1 1.0 O C:HOH380 4.7 41.2 1.0 C C:MET67 4.7 40.5 1.0 N C:ARG68 4.7 41.0 1.0 HB3 C:TYR71 4.7 35.9 1.0 CA C:ARG68 4.7 40.1 1.0 CB C:MET67 4.8 47.0 1.0 CA C:THR58 4.9 33.7 1.0 HG C:LEU56 4.9 34.2 1.0 HD22 C:LEU56 4.9 34.9 1.0 C23 C:21F202 4.9 26.7 0.4

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