Atomistry » Fluorine » PDB 5uv3-5vd4 » 5v9u
Atomistry »
  Fluorine »
    PDB 5uv3-5vd4 »
      5v9u »

Fluorine 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:

Calcium (Ca) 8 atoms
Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine 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 Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Small Molecule Ars-1620 Covalently Bound to K-Ras G12C, PDB code: 5v9u:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 5v9u

Go back to Fluorine Binding Sites List in 5v9u
Fluorine binding site 1 out of 4 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 Fluorine with other atoms in the F 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:F204

b:8.6
occ:1.00
F1 A:91S204 0.0 8.6 1.0
C13 A:91S204 1.4 7.4 1.0
C6 A:91S204 2.3 8.0 1.0
C12 A:91S204 2.3 6.8 1.0
N1 A:91S204 2.7 7.9 1.0
C5 A:91S204 2.7 8.9 1.0
O A:91S204 3.1 12.0 1.0
C A:91S204 3.1 9.4 1.0
O1 B:GOL206 3.2 25.1 1.0
NE2 A:HIS95 3.2 11.1 1.0
CG A:GLN99 3.4 9.7 1.0
O A:HOH333 3.4 16.7 1.0
C7 A:91S204 3.5 7.5 1.0
C9 A:91S204 3.6 7.2 1.0
O A:HOH371 3.6 16.9 0.5
C4 A:91S204 3.6 9.3 1.0
CB A:GLN99 3.8 8.6 1.0
CE1 A:HIS95 3.9 11.1 1.0
CD2 A:HIS95 4.0 10.6 1.0
C8 A:91S204 4.0 8.4 1.0
C11 A:91S204 4.0 8.2 1.0
F A:91S204 4.0 10.8 1.0
C1 A:91S204 4.2 10.6 1.0
CD A:GLN99 4.3 11.1 1.0
C1 B:GOL206 4.5 28.0 1.0
OE1 A:GLN99 4.5 13.1 1.0
CE1 A:TYR96 4.6 10.4 1.0
C3 A:91S204 4.7 9.3 1.0
C10 A:91S204 4.7 7.6 1.0
CD1 A:TYR96 4.7 9.6 1.0
ND1 A:HIS95 4.9 11.1 1.0
C2 A:91S204 4.9 8.5 1.0
N A:91S204 4.9 7.6 1.0
CG A:HIS95 5.0 10.0 1.0
O A:HOH371 5.0 21.5 0.5

Fluorine binding site 2 out of 4 in 5v9u

Go back to Fluorine Binding Sites List in 5v9u
Fluorine binding site 2 out of 4 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 Fluorine with other atoms in the F 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
A:F204

b:10.8
occ:1.00
F A:91S204 0.0 10.8 1.0
C4 A:91S204 1.4 9.3 1.0
C5 A:91S204 2.3 8.9 1.0
C3 A:91S204 2.5 9.3 1.0
C6 A:91S204 2.7 8.0 1.0
C7 A:91S204 3.3 7.5 1.0
CL A:91S204 3.4 10.8 1.0
CD1 A:TYR96 3.5 9.6 1.0
CE A:MET72 3.6 10.5 0.5
C A:91S204 3.6 9.4 1.0
C13 A:91S204 3.6 7.4 1.0
C2 A:91S204 3.7 8.5 1.0
CG1 A:VAL9 3.9 8.1 1.0
F1 A:91S204 4.0 8.6 1.0
CE1 A:TYR96 4.1 10.4 1.0
C1 A:91S204 4.1 10.6 1.0
CB A:VAL9 4.3 7.5 1.0
CG1 A:ILE100 4.3 8.3 1.0
C8 A:91S204 4.3 8.4 1.0
O A:TYR96 4.3 8.0 1.0
CB A:GLN99 4.4 8.6 1.0
CG A:TYR96 4.5 8.5 1.0
CA A:TYR96 4.5 7.8 1.0
CB A:TYR96 4.6 8.4 1.0
C12 A:91S204 4.7 6.8 1.0
SD A:MET72 4.7 12.8 0.5
CG2 A:VAL9 4.7 7.8 1.0
O A:91S204 4.7 12.0 1.0
CD1 A:ILE100 4.8 8.7 1.0
C A:TYR96 4.9 7.4 1.0
CG A:MET72 4.9 12.1 0.5
N A:ILE100 4.9 7.4 1.0
SD A:MET72 5.0 10.9 0.5
C9 A:91S204 5.0 7.2 1.0

Fluorine binding site 3 out of 4 in 5v9u

Go back to Fluorine Binding Sites List in 5v9u
Fluorine binding site 3 out of 4 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 Fluorine with other atoms in the F binding site number 3 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:F204

b:7.2
occ:1.00
F1 B:91S204 0.0 7.2 1.0
C13 B:91S204 1.3 6.5 1.0
C6 B:91S204 2.3 7.3 1.0
C12 B:91S204 2.3 6.4 1.0
N1 B:91S204 2.7 7.7 1.0
C5 B:91S204 2.7 9.8 1.0
O B:91S204 3.1 12.0 1.0
C B:91S204 3.1 9.7 1.0
O1 B:GOL201 3.2 21.2 1.0
NE2 B:HIS95 3.2 13.8 1.0
CG B:GLN99 3.5 13.1 1.0
O B:HOH319 3.5 17.2 0.5
C7 B:91S204 3.5 8.4 1.0
C9 B:91S204 3.6 6.5 1.0
C4 B:91S204 3.6 8.8 1.0
O B:HOH356 3.6 21.4 1.0
CB B:GLN99 3.8 11.5 1.0
CE1 B:HIS95 3.9 12.8 1.0
CD2 B:HIS95 4.0 12.4 1.0
F B:91S204 4.0 11.4 1.0
C11 B:91S204 4.0 7.9 1.0
C8 B:91S204 4.0 7.7 1.0
C1 B:91S204 4.2 10.5 1.0
C1 B:GOL201 4.4 20.3 1.0
CD B:GLN99 4.4 15.4 1.0
CE1 B:TYR96 4.5 11.2 1.0
CD1 B:TYR96 4.6 11.4 1.0
OE1 B:GLN99 4.6 16.4 1.0
C3 B:91S204 4.6 9.2 1.0
C10 B:91S204 4.7 7.4 1.0
C2 B:91S204 4.8 8.7 1.0
N B:91S204 4.9 8.4 1.0
ND1 B:HIS95 4.9 12.8 1.0
CL B:91S204 5.0 12.3 1.0
CG B:HIS95 5.0 11.8 1.0

Fluorine binding site 4 out of 4 in 5v9u

Go back to Fluorine Binding Sites List in 5v9u
Fluorine binding site 4 out of 4 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 Fluorine with other atoms in the F binding site number 4 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:F204

b:11.4
occ:1.00
F B:91S204 0.0 11.4 1.0
C4 B:91S204 1.4 8.8 1.0
C5 B:91S204 2.3 9.8 1.0
C3 B:91S204 2.5 9.2 1.0
C6 B:91S204 2.8 7.3 1.0
C7 B:91S204 3.3 8.4 1.0
CL B:91S204 3.3 12.3 1.0
CD1 B:TYR96 3.4 11.4 1.0
CE B:MET72 3.5 13.5 0.5
C B:91S204 3.6 9.7 1.0
C13 B:91S204 3.6 6.5 1.0
C2 B:91S204 3.7 8.7 1.0
CG1 B:VAL9 3.9 10.8 1.0
F1 B:91S204 4.0 7.2 1.0
CE1 B:TYR96 4.1 11.2 1.0
C1 B:91S204 4.2 10.5 1.0
CG1 B:ILE100 4.2 11.5 1.0
CB B:VAL9 4.2 9.9 1.0
O B:TYR96 4.4 9.3 1.0
C8 B:91S204 4.4 7.7 1.0
CB B:GLN99 4.4 11.5 1.0
CG B:TYR96 4.5 9.9 1.0
CG2 B:VAL9 4.6 9.8 1.0
SD B:MET72 4.6 12.5 0.5
CB B:TYR96 4.6 9.7 1.0
CA B:TYR96 4.6 9.3 1.0
CD1 B:ILE100 4.7 11.9 1.0
C12 B:91S204 4.7 6.4 1.0
CG B:MET72 4.7 12.6 0.5
O B:91S204 4.7 12.0 1.0
C B:TYR96 4.9 9.1 1.0
N B:ILE100 5.0 10.7 1.0
SD B:MET72 5.0 13.0 0.5

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: Tue Jul 15 08:31:47 2025

Last articles

K in 9IS7
K in 9HKX
K in 9HKY
K in 9HKW
K in 9HFO
K in 9HFN
K in 9HI3
K in 9HFM
K in 9HAC
K in 9GXH
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy