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Chlorine in PDB 5v9u: Crystal Structure of Small Molecule Ars-1620 Covalently Bound to K-Ras G12C

Protein crystallography data

The structure of Crystal Structure of Small Molecule Ars-1620 Covalently Bound to K-Ras G12C, PDB code: 5v9u was solved by M.R.Janes, J.Zhang, L.-S.Li, R.Hansen, U.Peters, X.Guo, Y.Chen, A.Babbar, S.J.Firdaus, J.Feng, J.H.Chen, S.Li, D.Brehmer, L.Darjania, S.Li, Y.O.Long, C.Thach, Y.Liu, A.Zarieh, T.Ely, J.M.Kucharski, L.V.Kessler, T.Wu, Y.Wang, Y.Yao, X.Deng, P.Zarrinkar, D.Dashyant, M.V.Lorenzi, D.Hu-Lowe, M.P.Patricelli, P.Ren, Y.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 60.03 / 1.38
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 33.440, 39.740, 61.780, 77.48, 81.97, 77.20
R / Rfree (%) 14.9 / 18.9

Other elements in 5v9u:

The structure of Crystal Structure of Small Molecule Ars-1620 Covalently Bound to K-Ras G12C also contains other interesting chemical elements:

Fluorine (F) 4 atoms
Calcium (Ca) 8 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Small Molecule Ars-1620 Covalently Bound to K-Ras G12C (pdb code 5v9u). 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 Ars-1620 Covalently Bound to K-Ras G12C, PDB code: 5v9u:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 5v9u

Go back to Chlorine Binding Sites List in 5v9u
Chlorine binding site 1 out of 2 in the Crystal Structure of Small Molecule Ars-1620 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 Ars-1620 Covalently Bound to K-Ras G12C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:10.8
occ:1.00
CL A:91S204 0.0 10.8 1.0
C7 A:91S204 1.8 7.5 1.0
C8 A:91S204 2.7 8.4 1.0
C6 A:91S204 2.7 8.0 1.0
C5 A:91S204 3.2 8.9 1.0
F A:91S204 3.4 10.8 1.0
C4 A:91S204 3.5 9.3 1.0
NE A:ARG68 3.6 15.2 1.0
CE A:MET72 3.6 10.5 0.5
CD A:ARG68 3.7 15.3 1.0
SD A:MET72 3.8 10.9 0.5
SD A:MET72 3.9 12.8 0.5
CZ A:ARG68 3.9 14.7 1.0
C13 A:91S204 3.9 7.4 1.0
C A:91S204 4.0 9.4 1.0
C9 A:91S204 4.0 7.2 1.0
CG2 A:THR58 4.0 9.2 1.0
CB A:THR58 4.1 8.7 1.0
OG1 A:THR58 4.1 8.7 1.0
O A:HOH383 4.2 9.9 1.0
CG A:ARG68 4.3 16.6 1.0
CG A:MET72 4.3 12.1 0.5
NH2 A:ARG68 4.3 15.7 1.0
CG A:MET72 4.4 11.1 0.5
NH1 A:ARG68 4.4 16.6 1.0
C12 A:91S204 4.5 6.8 1.0
O A:91S204 4.5 12.0 1.0
CG1 A:VAL9 4.5 8.1 1.0
C3 A:91S204 4.5 9.3 1.0
CE A:MET72 4.7 15.5 0.5
C1 A:91S204 4.9 10.6 1.0
C14 A:91S204 4.9 9.7 1.0
O A:HOH333 4.9 16.7 1.0

Chlorine binding site 2 out of 2 in 5v9u

Go back to Chlorine Binding Sites List in 5v9u
Chlorine binding site 2 out of 2 in the Crystal Structure of Small Molecule Ars-1620 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 Ars-1620 Covalently Bound to K-Ras G12C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl204

b:12.3
occ:1.00
CL B:91S204 0.0 12.3 1.0
C7 B:91S204 1.7 8.4 1.0
C8 B:91S204 2.6 7.7 1.0
C6 B:91S204 2.7 7.3 1.0
C5 B:91S204 3.1 9.8 1.0
F B:91S204 3.3 11.4 1.0
C4 B:91S204 3.5 8.8 1.0
CD B:ARG68 3.6 17.1 1.0
NE B:ARG68 3.6 18.6 1.0
CE B:MET72 3.7 13.5 0.5
SD B:MET72 3.8 12.5 0.5
C13 B:91S204 3.9 6.5 1.0
SD B:MET72 3.9 13.0 0.5
C B:91S204 3.9 9.7 1.0
C9 B:91S204 4.0 6.5 1.0
O B:HOH366 4.1 10.8 1.0
CG2 B:THR58 4.1 11.4 1.0
CZ B:ARG68 4.1 21.6 1.0
CB B:THR58 4.1 11.2 1.0
OG1 B:THR58 4.2 10.8 1.0
CG B:ARG68 4.2 17.9 1.0
CG1 B:VAL9 4.2 10.8 1.0
CG B:MET72 4.3 12.6 0.5
CG B:MET72 4.4 13.1 0.5
C12 B:91S204 4.4 6.4 1.0
NH2 B:ARG68 4.5 20.5 1.0
O B:91S204 4.5 12.0 1.0
C3 B:91S204 4.5 9.2 1.0
NH1 B:ARG68 4.6 20.9 1.0
CE B:MET72 4.7 14.7 0.5
CE1 B:TYR96 4.9 11.2 1.0
C1 B:91S204 4.9 10.5 1.0
O B:HOH356 4.9 21.4 1.0
CB B:VAL9 4.9 9.9 1.0
F1 B:91S204 5.0 7.2 1.0

Reference:

M.R.Janes, J.Zhang, L.S.Li, R.Hansen, U.Peters, X.Guo, Y.Chen, A.Babbar, S.J.Firdaus, L.Darjania, J.Feng, J.H.Chen, S.Li, S.Li, Y.O.Long, C.Thach, Y.Liu, A.Zarieh, T.Ely, J.M.Kucharski, L.V.Kessler, T.Wu, K.Yu, Y.Wang, Y.Yao, X.Deng, P.P.Zarrinkar, D.Brehmer, D.Dhanak, M.V.Lorenzi, D.Hu-Lowe, M.P.Patricelli, P.Ren, Y.Liu. Targeting Kras Mutant Cancers with A Covalent G12C-Specific Inhibitor. Cell V. 172 578 2018.
ISSN: ISSN 1097-4172
PubMed: 29373830
DOI: 10.1016/J.CELL.2018.01.006
Page generated: Sat Jul 12 09:47:32 2025

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