Fluorine in PDB 7mdp: Kras G12C in Complex with G-2897

All present enzymatic activity of Kras G12C in Complex with G-2897:
3.6.5.2;

The structure of Kras G12C in Complex with G-2897, PDB code: 7mdp was solved by A.Oh, Y.Frank, W.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.90 / 1.96
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	149.365, 68.919, 100.543, 90, 114.29, 90
R / Rfree (%)	19.5 / 22.9

The structure of Kras G12C in Complex with G-2897 also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Arsenic	(As)	4 atoms

The binding sites of Fluorine atom in the Kras G12C in Complex with G-2897 (pdb code 7mdp). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Kras G12C in Complex with G-2897, PDB code: 7mdp:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Kras G12C in Complex with G-2897


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Kras G12C in Complex with G-2897 within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:97.8 occ:0.82 F12 A:Z07201 0.0 97.8 0.8 C11 A:Z07201 1.4 97.3 0.8 F13 A:Z07201 2.3 95.5 0.8 F14 A:Z07201 2.3 99.2 0.8 C3 A:Z07201 2.4 95.8 0.8 C2 A:Z07201 2.8 90.6 0.8 C4 A:Z07201 3.5 99.2 0.8 OE1 A:GLU62 3.7 118.0 1.0 N9 A:Z07201 4.1 102.3 0.8 C1 A:Z07201 4.1 90.8 0.8 NH2 A:ARG68 4.3 84.0 1.0 CB A:THR58 4.4 63.7 1.0 SD A:MET72 4.4 91.0 1.0 CG2 A:THR58 4.5 62.2 1.0 OG1 A:THR58 4.5 66.5 1.0 CE1 A:TYR96 4.5 86.0 1.0 CD A:GLU62 4.5 118.5 1.0 CG1 A:VAL9 4.6 69.5 1.0 NE A:ARG68 4.6 88.8 1.0 CG A:GLU62 4.6 121.5 1.0 C5 A:Z07201 4.7 99.5 0.8 CB A:VAL9 4.8 71.4 1.0 CZ A:ARG68 4.9 84.5 1.0 C6 A:Z07201 4.9 94.5 0.8

Fluorine binding site 2 out of 3 in the Kras G12C in Complex with G-2897


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Kras G12C in Complex with G-2897 within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:95.5 occ:0.82 F13 A:Z07201 0.0 95.5 0.8 C11 A:Z07201 1.4 97.3 0.8 F12 A:Z07201 2.3 97.8 0.8 F14 A:Z07201 2.3 99.2 0.8 C3 A:Z07201 2.4 95.8 0.8 N9 A:Z07201 2.5 102.3 0.8 C4 A:Z07201 2.7 99.2 0.8 NE A:ARG68 3.5 88.8 1.0 C2 A:Z07201 3.7 90.6 0.8 C8 A:Z07201 3.7 105.1 0.8 CA A:GLU62 3.9 125.7 1.0 O A:GLU63 4.1 129.6 1.0 C5 A:Z07201 4.1 99.5 0.8 OE1 A:GLU62 4.1 118.0 1.0 CD A:ARG68 4.2 91.4 1.0 CG A:ARG68 4.2 91.6 1.0 C A:GLU62 4.4 126.0 1.0 N10 A:Z07201 4.4 104.3 0.8 CZ A:ARG68 4.4 84.5 1.0 NH2 A:ARG68 4.5 84.0 1.0 N A:GLU63 4.5 123.8 1.0 CG A:GLU62 4.5 121.5 1.0 O A:GLN61 4.5 132.3 1.0 CB A:GLU62 4.6 123.0 1.0 C1 A:Z07201 4.8 90.8 0.8 SD A:MET72 4.8 91.0 1.0 CD A:GLU62 4.8 118.5 1.0 S7 A:Z07201 4.9 107.8 0.8 N A:GLU62 4.9 127.5 1.0 C6 A:Z07201 4.9 94.5 0.8 CE1 A:TYR64 5.0 135.7 1.0

Fluorine binding site 3 out of 3 in the Kras G12C in Complex with G-2897


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Kras G12C in Complex with G-2897 within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:99.2 occ:0.82 F14 A:Z07201 0.0 99.2 0.8 C11 A:Z07201 1.4 97.3 0.8 F13 A:Z07201 2.3 95.5 0.8 F12 A:Z07201 2.3 97.8 0.8 C3 A:Z07201 2.3 95.8 0.8 C2 A:Z07201 3.0 90.6 0.8 CG A:GLU62 3.0 121.5 1.0 C4 A:Z07201 3.3 99.2 0.8 OE1 A:GLU62 3.4 118.0 1.0 CB A:GLU62 3.6 123.0 1.0 CD A:GLU62 3.7 118.5 1.0 N9 A:Z07201 3.7 102.3 0.8 CE1 A:TYR96 3.8 86.0 1.0 CA A:GLU62 3.9 125.7 1.0 C1 A:Z07201 4.3 90.8 0.8 CD1 A:TYR96 4.3 84.9 1.0 C5 A:Z07201 4.4 99.5 0.8 C A:GLU62 4.7 126.0 1.0 CZ A:TYR96 4.7 89.1 1.0 CE1 A:TYR64 4.8 135.7 1.0 OH A:TYR64 4.8 135.4 1.0 C6 A:Z07201 4.8 94.5 0.8 OE2 A:GLU62 4.9 117.0 1.0 OH A:TYR96 4.9 92.8 1.0 C8 A:Z07201 4.9 105.1 0.8 N A:GLU62 5.0 127.5 1.0

C.W.Davies, A.J.Oh, R.Mroue, M.Steffek, J.M.Bruning, Y.Xiao, S.Feng, S.Jayakar, E.Chan, V.Arumugam, S.C.Uribe, J.Drummond, A.Frommlet, C.Lu, Y.Franke, M.Merchant, H.Koeppen, J.G.Quinn, S.Malhotra, S.Do, L.Gazzard, H.E.Purkey, J.Rudolph, M.M.Mulvihill, J.T.Koerber, W.Wang, M.Evangelista. Conformation-Locking Antibodies For the Discovery and Characterization of Kras Inhibitors. Nat.Biotechnol. V. 40 769 2022.
ISSN: ISSN 1087-0156
PubMed: 34992247
DOI: 10.1038/S41587-021-01126-9