Fluorine in PDB 7jv0: Crystal Structure of KSR1:MEK1 in Complex with Amp-Pnp, and Allosteric Mek Inhibitor PD0325901

Enzymatic activity of Crystal Structure of KSR1:MEK1 in Complex with Amp-Pnp, and Allosteric Mek Inhibitor PD0325901

All present enzymatic activity of Crystal Structure of KSR1:MEK1 in Complex with Amp-Pnp, and Allosteric Mek Inhibitor PD0325901:
2.7.11.1; 2.7.12.2;

Protein crystallography data

The structure of Crystal Structure of KSR1:MEK1 in Complex with Amp-Pnp, and Allosteric Mek Inhibitor PD0325901, PDB code: 7jv0 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) 40.00 / 3.63
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 137.660, 137.660, 220.890, 90.00, 90.00, 120.00
R / Rfree (%) 24.6 / 26

Other elements in 7jv0:

The structure of Crystal Structure of KSR1:MEK1 in Complex with Amp-Pnp, and Allosteric Mek Inhibitor PD0325901 also contains other interesting chemical elements:

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

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of KSR1:MEK1 in Complex with Amp-Pnp, and Allosteric Mek Inhibitor PD0325901 (pdb code 7jv0). 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 KSR1:MEK1 in Complex with Amp-Pnp, and Allosteric Mek Inhibitor PD0325901, PDB code: 7jv0:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7jv0

Go back to Fluorine Binding Sites List in 7jv0
Fluorine binding site 1 out of 3 in the Crystal Structure of KSR1:MEK1 in Complex with Amp-Pnp, and Allosteric Mek Inhibitor PD0325901


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 KSR1:MEK1 in Complex with Amp-Pnp, and Allosteric Mek Inhibitor PD0325901 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F402

b:0.5
occ:1.00
 F24 C:4BM402 0.0 0.5 1.0
C06 C:4BM402 1.4 0.8 1.0
C01 C:4BM402 2.4 0.4 1.0
C05 C:4BM402 2.4 0.2 1.0
N07 C:4BM402 2.8 0.6 1.0
OD1 C:ASP208 3.1 0.2 1.0
CE C:MET143 3.2 1.0 1.0
O16 C:4BM402 3.3 0.4 1.0
C02 C:4BM402 3.7 0.1 1.0
C04 C:4BM402 3.7 0.1 1.0
CG2 C:ILE141 3.8 0.6 1.0
CD C:LYS97 4.0 0.7 1.0
C03 C:4BM402 4.2 0.9 1.0
CB C:ILE141 4.2 0.5 1.0
CG C:ASP208 4.2 0.5 1.0
C08 C:4BM402 4.2 0.2 1.0
CG1 C:ILE141 4.3 0.6 1.0
CA C:ASP208 4.4 0.9 1.0
C14 C:4BM402 4.4 0.5 1.0
N C:ASP208 4.4 0.4 1.0
CE C:LYS97 4.7 0.8 1.0
C09 C:4BM402 4.8 0.5 1.0
SD C:MET143 4.9 0.3 1.0
CB C:ASP208 4.9 0.0 1.0

Fluorine binding site 2 out of 3 in 7jv0

Go back to Fluorine Binding Sites List in 7jv0
Fluorine binding site 2 out of 3 in the Crystal Structure of KSR1:MEK1 in Complex with Amp-Pnp, and Allosteric Mek Inhibitor PD0325901


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 KSR1:MEK1 in Complex with Amp-Pnp, and Allosteric Mek Inhibitor PD0325901 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F402

b:0.6
occ:1.00
 F25 C:4BM402 0.0 0.6 1.0
C13 C:4BM402 1.3 0.3 1.0
C12 C:4BM402 2.3 0.0 1.0
C08 C:4BM402 2.4 0.2 1.0
F26 C:4BM402 2.7 0.2 1.0
C02 C:4BM402 2.8 0.1 1.0
N07 C:4BM402 2.9 0.6 1.0
CG1 C:VAL211 3.0 0.2 1.0
C01 C:4BM402 3.2 0.4 1.0
C11 C:4BM402 3.6 0.6 1.0
C09 C:4BM402 3.6 0.5 1.0
O C:PHE209 3.7 0.1 1.0
C03 C:4BM402 4.0 0.9 1.0
C10 C:4BM402 4.1 0.7 1.0
CD2 C:LEU215 4.1 0.4 1.0
CD1 C:LEU115 4.2 0.3 1.0
N C:VAL211 4.2 0.3 1.0
CB C:VAL211 4.4 0.5 1.0
CG C:LEU115 4.4 0.2 1.0
C06 C:4BM402 4.5 0.8 1.0
CD1 C:LEU118 4.6 0.1 1.0
N C:SER212 4.7 0.1 1.0
CA C:VAL211 4.8 0.1 1.0
C C:PHE209 4.9 0.2 1.0
C14 C:4BM402 4.9 0.5 1.0

Fluorine binding site 3 out of 3 in 7jv0

Go back to Fluorine Binding Sites List in 7jv0
Fluorine binding site 3 out of 3 in the Crystal Structure of KSR1:MEK1 in Complex with Amp-Pnp, and Allosteric Mek Inhibitor PD0325901


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 KSR1:MEK1 in Complex with Amp-Pnp, and Allosteric Mek Inhibitor PD0325901 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F402

b:0.2
occ:1.00
 F26 C:4BM402 0.0 0.2 1.0
C12 C:4BM402 1.4 0.0 1.0
C13 C:4BM402 2.4 0.3 1.0
C11 C:4BM402 2.4 0.6 1.0
F25 C:4BM402 2.7 0.6 1.0
N C:SER212 2.9 0.1 1.0
N C:VAL211 2.9 0.3 1.0
CG1 C:VAL211 3.4 0.2 1.0
C C:GLY210 3.6 0.1 1.0
C08 C:4BM402 3.6 0.2 1.0
C10 C:4BM402 3.6 0.7 1.0
O C:SER212 3.7 0.9 1.0
CB C:SER212 3.7 0.6 1.0
CA C:GLY210 3.7 0.2 1.0
O C:PHE209 3.7 0.1 1.0
CA C:SER212 3.7 0.6 1.0
CA C:VAL211 3.7 0.1 1.0
C C:VAL211 3.7 0.5 1.0
CD2 C:LEU215 3.8 0.4 1.0
C09 C:4BM402 4.1 0.5 1.0
C C:SER212 4.2 0.1 1.0
CB C:VAL211 4.2 0.5 1.0
CG C:LEU215 4.5 0.8 1.0
C C:PHE209 4.5 0.2 1.0
O C:GLY210 4.6 0.6 1.0
N C:GLY210 4.6 0.0 1.0
OG C:SER212 4.7 0.7 1.0
CB C:LEU215 4.8 0.7 1.0
N07 C:4BM402 4.9 0.6 1.0
O C:VAL211 4.9 0.1 1.0
CG1 C:ILE216 5.0 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 08:03:45 2024

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