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Fluorine in PDB 6pgp: Crystal Structure of Human Kras G12C Covalently Bound to A Quinazolinone Inhibitor

Protein crystallography data

The structure of Crystal Structure of Human Kras G12C Covalently Bound to A Quinazolinone Inhibitor, PDB code: 6pgp was solved by C.Mohr, D.A.Whittington, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.00 / 1.50
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 33.420, 39.606, 62.451, 76.91, 81.38, 77.30
R / Rfree (%) 19 / 21.6

Other elements in 6pgp:

The structure of Crystal Structure of Human Kras G12C Covalently Bound to A Quinazolinone Inhibitor also contains other interesting chemical elements:

Calcium (Ca) 4 atoms
Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Kras G12C Covalently Bound to A Quinazolinone Inhibitor (pdb code 6pgp). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of Human Kras G12C Covalently Bound to A Quinazolinone Inhibitor, PDB code: 6pgp:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 6pgp

Go back to Fluorine Binding Sites List in 6pgp
Fluorine binding site 1 out of 2 in the Crystal Structure of Human Kras G12C Covalently Bound to A Quinazolinone Inhibitor


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 Human Kras G12C Covalently Bound to A Quinazolinone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F504

b:17.5
occ:1.00
F1 A:OHY504 0.0 17.5 1.0
C20 A:OHY504 1.3 17.6 1.0
C19 A:OHY504 2.4 17.9 1.0
C7 A:OHY504 2.4 17.9 1.0
C4 A:OHY504 2.8 17.3 1.0
C5 A:OHY504 3.2 17.2 1.0
CL1 A:OHY504 3.2 18.1 1.0
CD1 A:TYR96 3.3 11.2 1.0
C18 A:OHY504 3.6 18.0 1.0
C16 A:OHY504 3.6 18.1 1.0
CG1 A:VAL9 3.7 10.1 1.0
C3 A:OHY504 3.8 17.4 1.0
CE1 A:TYR96 3.9 11.3 1.0
CB A:VAL9 4.0 9.9 1.0
C17 A:OHY504 4.1 18.5 1.0
C6 A:OHY504 4.3 16.9 1.0
CG2 A:VAL9 4.4 10.0 1.0
CG A:TYR96 4.4 11.1 1.0
CG1 A:ILE100 4.5 12.3 1.0
O A:TYR96 4.5 10.7 1.0
CB A:GLN99 4.6 11.9 1.0
CB A:TYR96 4.6 11.0 1.0
SD A:MET72 4.7 19.6 1.0
C2 A:OHY504 4.7 17.5 1.0
O2 A:OHY504 4.8 19.2 1.0
CA A:TYR96 4.8 11.1 1.0
O A:HOH649 4.8 12.9 1.0
CD1 A:ILE100 5.0 11.9 1.0
C1 A:OHY504 5.0 17.5 1.0
CG A:MET72 5.0 19.0 1.0

Fluorine binding site 2 out of 2 in 6pgp

Go back to Fluorine Binding Sites List in 6pgp
Fluorine binding site 2 out of 2 in the Crystal Structure of Human Kras G12C Covalently Bound to A Quinazolinone Inhibitor


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 Human Kras G12C Covalently Bound to A Quinazolinone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F504

b:16.1
occ:1.00
F1 B:OHY504 0.0 16.1 1.0
C20 B:OHY504 1.3 16.3 1.0
C19 B:OHY504 2.4 16.6 1.0
C7 B:OHY504 2.4 16.6 1.0
C4 B:OHY504 2.8 16.2 1.0
C5 B:OHY504 3.2 16.0 1.0
CL1 B:OHY504 3.3 16.4 1.0
CD1 B:TYR96 3.4 13.5 1.0
C18 B:OHY504 3.6 16.6 1.0
C16 B:OHY504 3.6 17.1 1.0
C3 B:OHY504 3.7 16.2 1.0
CG1 B:VAL9 3.8 11.1 1.0
CE1 B:TYR96 3.9 13.8 1.0
CB B:VAL9 4.0 10.9 1.0
C17 B:OHY504 4.1 17.3 1.0
C6 B:OHY504 4.3 16.2 1.0
CG B:TYR96 4.5 13.0 1.0
CG2 B:VAL9 4.5 11.1 1.0
O B:TYR96 4.5 11.9 1.0
CB B:GLN99 4.5 10.9 1.0
CG1 B:ILE100 4.6 11.9 1.0
CB B:TYR96 4.7 12.3 1.0
C2 B:OHY504 4.7 16.7 1.0
O B:HOH655 4.8 13.1 1.0
O2 B:OHY504 4.8 18.9 1.0
CA B:TYR96 4.8 12.2 1.0
SD B:MET72 4.8 19.1 1.0
C1 B:OHY504 5.0 16.5 1.0

Reference:

B.A.Lanman, J.R.Allen, J.G.Allen, A.K.Amegadzie, K.S.Ashton, S.K.Booker, J.J.Chen, N.Chen, M.J.Frohn, G.Goodman, D.J.Kopecky, L.Liu, P.Lopez, J.D.Low, V.Ma, A.E.Minatti, T.T.Nguyen, N.Nishimura, A.J.Pickrell, A.B.Reed, Y.Shin, A.Siegmund, N.A.Tamayo, C.M.Tegley, M.C.Walton, H.L.Wang, R.P.Wurz, M.Xue, K.C.Yang, P.Achanta, M.D.Bartberger, J.Canon, L.S.Hollis, J.D.Mccarter, C.Mohr, K.Rex, A.Y.Saiki, T.San Miguel, L.Volak, K.H.Wang, D.A.Whittington, S.G.Zech, J.R.Lipford, V.J.Cee. Discovery of A Covalent Inhibitor of KRASG12C (Amg 510) For the Treatment of Solid Tumors. J.Med.Chem. 2019.
ISSN: ISSN 0022-2623
PubMed: 31820981
DOI: 10.1021/ACS.JMEDCHEM.9B01180
Page generated: Fri Aug 2 00:25:40 2024

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