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Fluorine in PDB 7jus: Crystal Structure of KSR2:MEK1 in Complex with Amp-Pnp, and Allosteric Mek Inhibitor Cobimetinib

Enzymatic activity of Crystal Structure of KSR2:MEK1 in Complex with Amp-Pnp, and Allosteric Mek Inhibitor Cobimetinib

All present enzymatic activity of Crystal Structure of KSR2:MEK1 in Complex with Amp-Pnp, and Allosteric Mek Inhibitor Cobimetinib:
2.7.11.1; 2.7.12.2;

Protein crystallography data

The structure of Crystal Structure of KSR2:MEK1 in Complex with Amp-Pnp, and Allosteric Mek Inhibitor Cobimetinib, PDB code: 7jus was solved by Z.M.Khan, A.C.Dar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.72 / 2.99
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 140.000, 140.000, 220.000, 90.00, 90.00, 120.00
R / Rfree (%) 24.8 / 26.5

Other elements in 7jus:

The structure of Crystal Structure of KSR2:MEK1 in Complex with Amp-Pnp, and Allosteric Mek Inhibitor Cobimetinib also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Iodine (I) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of KSR2:MEK1 in Complex with Amp-Pnp, and Allosteric Mek Inhibitor Cobimetinib (pdb code 7jus). 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 KSR2:MEK1 in Complex with Amp-Pnp, and Allosteric Mek Inhibitor Cobimetinib, PDB code: 7jus:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7jus

Go back to Fluorine Binding Sites List in 7jus
Fluorine binding site 1 out of 3 in the Crystal Structure of KSR2:MEK1 in Complex with Amp-Pnp, and Allosteric Mek Inhibitor Cobimetinib


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 KSR2:MEK1 in Complex with Amp-Pnp, and Allosteric Mek Inhibitor Cobimetinib within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F501

b:0.9
occ:1.00
 F07 C:VKD501 0.0 0.9 1.0
C06 C:VKD501 1.4 0.1 1.0
C05 C:VKD501 2.4 0.9 1.0
C08 C:VKD501 2.4 0.0 1.0
F09 C:VKD501 2.7 0.7 1.0
CG2 C:VAL211 3.3 0.9 1.0
N C:SER212 3.5 0.4 1.0
N C:VAL211 3.5 0.5 1.0
C04 C:VKD501 3.6 0.6 1.0
CD1 C:LEU215 3.7 0.3 1.0
C10 C:VKD501 3.7 0.7 1.0
CB C:SER212 3.8 0.7 1.0
O C:PHE209 3.9 0.8 1.0
CA C:SER212 4.2 0.2 1.0
O C:SER212 4.2 1.0 1.0
CA C:VAL211 4.2 0.9 1.0
C03 C:VKD501 4.2 0.1 1.0
CB C:VAL211 4.2 0.8 1.0
C C:VAL211 4.3 0.4 1.0
CD2 C:LEU115 4.3 1.0 1.0
C C:GLY210 4.4 0.3 1.0
CB C:LEU215 4.4 0.0 1.0
CG C:LEU215 4.5 0.6 1.0
CG1 C:VAL211 4.5 0.9 1.0
CA C:GLY210 4.5 0.7 1.0
C C:SER212 4.6 0.7 1.0
CD2 C:LEU215 4.8 0.6 1.0
OG C:SER212 4.8 0.5 1.0
N11 C:VKD501 4.9 0.1 1.0
C C:PHE209 4.9 0.1 1.0
C13 C:VKD501 5.0 0.4 1.0

Fluorine binding site 2 out of 3 in 7jus

Go back to Fluorine Binding Sites List in 7jus
Fluorine binding site 2 out of 3 in the Crystal Structure of KSR2:MEK1 in Complex with Amp-Pnp, and Allosteric Mek Inhibitor Cobimetinib


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 KSR2:MEK1 in Complex with Amp-Pnp, and Allosteric Mek Inhibitor Cobimetinib within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F501

b:0.7
occ:1.00
 F09 C:VKD501 0.0 0.7 1.0
C08 C:VKD501 1.4 0.0 1.0
C06 C:VKD501 2.4 0.1 1.0
C10 C:VKD501 2.4 0.7 1.0
C13 C:VKD501 2.7 0.4 1.0
F07 C:VKD501 2.7 0.9 1.0
N11 C:VKD501 2.9 0.1 1.0
C12 C:VKD501 3.0 0.2 1.0
CD1 C:ILE141 3.4 0.0 1.0
CD2 C:LEU115 3.6 1.0 1.0
C05 C:VKD501 3.6 0.9 1.0
C03 C:VKD501 3.7 0.1 1.0
C14 C:VKD501 3.7 0.3 1.0
CG2 C:VAL211 3.8 0.9 1.0
O C:PHE209 4.0 0.8 1.0
C04 C:VKD501 4.1 0.6 1.0
C18 C:VKD501 4.2 1.0 1.0
CD1 C:LEU118 4.4 0.0 1.0
CD1 C:LEU215 4.4 0.3 1.0
CG1 C:VAL211 4.5 0.9 1.0
C15 C:VKD501 4.7 0.8 1.0
CB C:VAL211 4.8 0.8 1.0
CG1 C:ILE141 4.8 0.4 1.0
C17 C:VKD501 4.9 0.4 1.0
C02 C:VKD501 5.0 0.4 1.0
N C:VAL211 5.0 0.5 1.0

Fluorine binding site 3 out of 3 in 7jus

Go back to Fluorine Binding Sites List in 7jus
Fluorine binding site 3 out of 3 in the Crystal Structure of KSR2:MEK1 in Complex with Amp-Pnp, and Allosteric Mek Inhibitor Cobimetinib


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 KSR2:MEK1 in Complex with Amp-Pnp, and Allosteric Mek Inhibitor Cobimetinib within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F501

b:0.8
occ:1.00
 F19 C:VKD501 0.0 0.8 1.0
C18 C:VKD501 1.4 1.0 1.0
C12 C:VKD501 2.4 0.2 1.0
C17 C:VKD501 2.4 0.4 1.0
OD2 C:ASP208 2.8 0.1 1.0
N11 C:VKD501 2.8 0.1 1.0
C13 C:VKD501 3.6 0.4 1.0
C15 C:VKD501 3.7 0.8 1.0
CG C:ASP208 4.0 0.8 1.0
SD C:MET143 4.0 0.5 1.0
CG2 C:ILE141 4.1 0.4 1.0
O01 C:VKD501 4.1 0.9 1.0
CD C:LYS97 4.1 0.9 1.0
C14 C:VKD501 4.2 0.3 1.0
C10 C:VKD501 4.3 0.7 1.0
CE C:LYS97 4.4 0.6 1.0
CE C:MET143 4.5 0.4 1.0
CB C:ILE141 4.5 0.6 1.0
CA C:ASP208 4.5 0.4 1.0
CD1 C:ILE141 4.5 0.0 1.0
SG C:CYS207 4.6 0.3 1.0
N C:ASP208 4.6 0.4 1.0
CB C:LYS97 4.7 0.2 1.0
OD1 C:ASP208 4.7 0.6 1.0
CG C:LYS97 4.7 0.5 1.0
CB C:ASP208 4.8 0.4 1.0
C02 C:VKD501 4.9 0.4 1.0

Reference:

Z.M.Khan, A.M.Real, W.M.Marsiglia, A.Chow, M.E.Duffy, J.R.Yerabolu, A.P.Scopton, A.C.Dar. Structural Basis For the Action of the Drug Trametinib at Ksr-Bound Mek. Nature 2020.
ISSN: ESSN 1476-4687
PubMed: 32927473
DOI: 10.1038/S41586-020-2760-4
Page generated: Fri Aug 2 08:03:05 2024

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