Fluorine in PDB 8wb1: Crystal Structure of Small Molecule KN2H Covalently Bound to K- Ras(G12D)

The structure of Crystal Structure of Small Molecule KN2H Covalently Bound to K- Ras(G12D), PDB code: 8wb1 was solved by L.Zhou, R.Zhang, T.B.Shuai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.98 / 1.72
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	40.099, 51.955, 90.475, 90, 90, 90
R / Rfree (%)	19.2 / 21.2

The structure of Crystal Structure of Small Molecule KN2H Covalently Bound to K- Ras(G12D) also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Fluorine atom in the Crystal Structure of Small Molecule KN2H Covalently Bound to K- Ras(G12D) (pdb code 8wb1). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Small Molecule KN2H Covalently Bound to K- Ras(G12D), PDB code: 8wb1:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of Small Molecule KN2H Covalently Bound to K- Ras(G12D)


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 KN2H Covalently Bound to K- Ras(G12D) within 5.0Å range: probe atom residue distance (Å) B Occ A:F204 b:34.5 occ:1.00 F01 A:W3T204 0.0 34.5 1.0 C02 A:W3T204 1.4 33.6 1.0 C55 A:W3T204 2.2 30.9 1.0 C03 A:W3T204 2.4 30.1 1.0 N51 A:W3T204 2.8 30.7 1.0 C04 A:W3T204 2.9 28.6 1.0 C54 A:W3T204 3.2 31.4 1.0 C52 A:W3T204 3.4 31.7 1.0 O A:HOH328 3.5 39.6 1.0 C53 A:W3T204 3.8 31.1 1.0 OD1 A:ASP92 3.9 32.4 1.0 NZ A:LYS88 4.2 37.7 1.0 C05 A:W3T204 4.5 30.3 1.0 CG A:ASP92 4.6 34.1 1.0 O06 A:W3T204 4.7 28.2 1.0 CG A:HIS95 4.9 29.4 1.0 OD2 A:ASP92 5.0 31.3 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Small Molecule KN2H Covalently Bound to K- Ras(G12D)


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 KN2H Covalently Bound to K- Ras(G12D) within 5.0Å range: probe atom residue distance (Å) B Occ A:F204 b:28.6 occ:1.00 F32 A:W3T204 0.0 28.6 1.0 C31 A:W3T204 1.4 27.5 1.0 C30 A:W3T204 2.4 27.0 1.0 C33 A:W3T204 2.5 28.2 1.0 N50 A:W3T204 2.8 25.9 1.0 C34 A:W3T204 2.8 26.8 1.0 C35 A:W3T204 3.1 26.5 1.0 C37 A:W3T204 3.2 25.4 1.0 CE1 A:TYR64 3.3 28.5 1.0 C36 A:W3T204 3.3 22.6 1.0 NE2 A:HIS95 3.3 27.9 1.0 OH A:TYR64 3.5 27.9 1.0 C47 A:W3T204 3.5 26.3 1.0 C29 A:W3T204 3.6 24.8 1.0 C38 A:W3T204 3.6 28.2 1.0 N48 A:W3T204 3.7 27.7 1.0 CG A:GLN99 3.7 24.6 1.0 CZ A:TYR64 3.7 28.7 1.0 CE1 A:HIS95 4.0 29.0 1.0 C07 A:W3T204 4.1 27.3 1.0 C49 A:W3T204 4.1 26.9 1.0 C43 A:W3T204 4.1 24.4 1.0 CB A:GLN99 4.2 25.0 1.0 CD2 A:HIS95 4.2 27.2 1.0 CD1 A:TYR64 4.3 29.5 1.0 C39 A:W3T204 4.4 25.9 1.0 CE1 A:TYR96 4.4 24.2 1.0 C45 A:W3T204 4.5 27.3 1.0 CD1 A:TYR96 4.6 27.0 1.0 CD A:GLN99 4.6 30.3 1.0 C44 A:W3T204 4.7 26.2 1.0 OE1 A:GLN99 4.8 27.7 1.0 C09 A:W3T204 4.8 27.1 1.0 N08 A:W3T204 4.9 25.3 1.0 O06 A:W3T204 5.0 28.2 1.0 CE2 A:TYR64 5.0 29.4 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Small Molecule KN2H Covalently Bound to K- Ras(G12D)


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 KN2H Covalently Bound to K- Ras(G12D) within 5.0Å range: probe atom residue distance (Å) B Occ A:F204 b:25.7 occ:1.00 F40 A:W3T204 0.0 25.7 1.0 C39 A:W3T204 1.4 25.9 1.0 C36 A:W3T204 2.4 22.6 1.0 C41 A:W3T204 2.4 25.2 1.0 C37 A:W3T204 2.7 25.4 1.0 C38 A:W3T204 3.4 28.2 1.0 CG1 A:VAL9 3.4 23.6 1.0 CG1 A:ILE100 3.6 23.3 1.0 C42 A:W3T204 3.7 27.4 1.0 C35 A:W3T204 3.7 26.5 1.0 CB A:VAL9 3.8 21.3 1.0 CG2 A:VAL9 4.0 21.4 1.0 C43 A:W3T204 4.1 24.4 1.0 O A:TYR96 4.2 25.0 1.0 CD1 A:ILE100 4.2 24.6 1.0 CD1 A:TYR96 4.3 27.0 1.0 SD A:MET72 4.5 33.2 1.0 CE2 A:PHE78 4.6 21.8 1.0 CD2 A:PHE78 4.6 22.6 1.0 CB A:GLN99 4.6 25.0 1.0 N A:ILE100 4.7 26.1 1.0 CB A:TYR96 4.7 27.2 1.0 CA A:TYR96 4.8 24.5 1.0 C A:TYR96 4.9 26.8 1.0 C34 A:W3T204 4.9 26.8 1.0 CB A:ILE100 4.9 27.3 1.0 CG A:TYR96 5.0 23.8 1.0

L.Zhou, R.Zhang, T.B.Shuai. Crystal Structure of Small Molecule KN2H Covalently Bound to K-Ras(G12D) To Be Published.