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Fluorine in PDB 3dy7: X-Ray Structure of the Human Mitogen-Activated Protein Kinase Kinase 1 (MEK1) in A Complex with Ligand and Mgatp

Enzymatic activity of X-Ray Structure of the Human Mitogen-Activated Protein Kinase Kinase 1 (MEK1) in A Complex with Ligand and Mgatp

All present enzymatic activity of X-Ray Structure of the Human Mitogen-Activated Protein Kinase Kinase 1 (MEK1) in A Complex with Ligand and Mgatp:
2.7.12.2;

Protein crystallography data

The structure of X-Ray Structure of the Human Mitogen-Activated Protein Kinase Kinase 1 (MEK1) in A Complex with Ligand and Mgatp, PDB code: 3dy7 was solved by J.F.Ohren, A.Pavlovsky, E.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.70
Space group P 62
Cell size a, b, c (Å), α, β, γ (°) 81.754, 81.754, 128.893, 90.00, 90.00, 120.00
R / Rfree (%) 24.7 / 26.9

Other elements in 3dy7:

The structure of X-Ray Structure of the Human Mitogen-Activated Protein Kinase Kinase 1 (MEK1) in A Complex with Ligand and Mgatp 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 X-Ray Structure of the Human Mitogen-Activated Protein Kinase Kinase 1 (MEK1) in A Complex with Ligand and Mgatp (pdb code 3dy7). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the X-Ray Structure of the Human Mitogen-Activated Protein Kinase Kinase 1 (MEK1) in A Complex with Ligand and Mgatp, PDB code: 3dy7:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 3dy7

Go back to Fluorine Binding Sites List in 3dy7
Fluorine binding site 1 out of 3 in the X-Ray Structure of the Human Mitogen-Activated Protein Kinase Kinase 1 (MEK1) in A Complex with Ligand and Mgatp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of X-Ray Structure of the Human Mitogen-Activated Protein Kinase Kinase 1 (MEK1) in A Complex with Ligand and Mgatp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F9002

b:58.6
occ:1.00
F1 A:1CX9002 0.0 58.6 1.0
C10 A:1CX9002 1.3 58.7 1.0
C11 A:1CX9002 2.3 58.3 1.0
C9 A:1CX9002 2.3 58.5 1.0
F2 A:1CX9002 2.7 58.5 1.0
N A:SER212 3.2 61.5 1.0
N A:VAL211 3.2 59.5 1.0
O A:PHE209 3.4 57.3 1.0
C12 A:1CX9002 3.6 59.4 1.0
C8 A:1CX9002 3.6 58.1 1.0
CG2 A:VAL211 3.8 60.6 1.0
CA A:GLY210 3.8 58.2 1.0
C A:GLY210 3.9 59.0 1.0
CB A:SER212 3.9 62.3 1.0
O A:SER212 4.0 63.2 1.0
CA A:SER212 4.0 62.3 1.0
CD2 A:LEU215 4.0 68.2 1.0
CA A:VAL211 4.1 60.1 1.0
C7 A:1CX9002 4.1 60.7 1.0
C A:VAL211 4.1 60.7 1.0
CB A:VAL211 4.3 60.3 1.0
C A:PHE209 4.3 57.2 1.0
C A:SER212 4.5 62.9 1.0
CB A:LEU215 4.6 69.2 1.0
N1 A:1CX9002 4.6 59.2 1.0
N A:GLY210 4.6 57.5 1.0
CD1 A:LEU115 4.6 67.7 1.0
CG A:LEU215 4.6 68.2 1.0
C4 A:1CX9002 4.7 64.7 1.0
CG1 A:ILE216 4.8 73.3 1.0
O A:GLY210 4.9 59.6 1.0
CD1 A:ILE216 5.0 74.5 1.0
OG A:SER212 5.0 61.7 1.0

Fluorine binding site 2 out of 3 in 3dy7

Go back to Fluorine Binding Sites List in 3dy7
Fluorine binding site 2 out of 3 in the X-Ray Structure of the Human Mitogen-Activated Protein Kinase Kinase 1 (MEK1) in A Complex with Ligand and Mgatp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of X-Ray Structure of the Human Mitogen-Activated Protein Kinase Kinase 1 (MEK1) in A Complex with Ligand and Mgatp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F9002

b:58.5
occ:1.00
F2 A:1CX9002 0.0 58.5 1.0
C11 A:1CX9002 1.3 58.3 1.0
C12 A:1CX9002 2.2 59.4 1.0
C10 A:1CX9002 2.3 58.7 1.0
C4 A:1CX9002 2.4 64.7 1.0
N1 A:1CX9002 2.4 59.2 1.0
C3 A:1CX9002 2.6 64.5 1.0
F1 A:1CX9002 2.7 58.6 1.0
C7 A:1CX9002 3.5 60.7 1.0
C9 A:1CX9002 3.6 58.5 1.0
C5 A:1CX9002 3.6 65.7 1.0
O A:PHE209 3.6 57.3 1.0
CG2 A:VAL211 3.7 60.6 1.0
C2 A:1CX9002 3.8 66.5 1.0
CD1 A:LEU115 3.9 67.7 1.0
CD1 A:ILE141 4.0 66.6 1.0
C8 A:1CX9002 4.0 58.1 1.0
CD2 A:LEU215 4.3 68.2 1.0
F3 A:1CX9002 4.5 63.1 1.0
CD1 A:LEU118 4.5 65.8 1.0
C6 A:1CX9002 4.6 66.9 1.0
C1 A:1CX9002 4.6 66.1 1.0
C13 A:1CX9002 4.7 62.4 1.0
N A:VAL211 4.8 59.5 1.0
CB A:VAL211 4.8 60.3 1.0
C A:PHE209 4.8 57.2 1.0
O1 A:1CX9002 4.9 61.7 1.0

Fluorine binding site 3 out of 3 in 3dy7

Go back to Fluorine Binding Sites List in 3dy7
Fluorine binding site 3 out of 3 in the X-Ray Structure of the Human Mitogen-Activated Protein Kinase Kinase 1 (MEK1) in A Complex with Ligand and Mgatp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of X-Ray Structure of the Human Mitogen-Activated Protein Kinase Kinase 1 (MEK1) in A Complex with Ligand and Mgatp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F9002

b:63.1
occ:1.00
F3 A:1CX9002 0.0 63.1 1.0
C2 A:1CX9002 1.3 66.5 1.0
C3 A:1CX9002 2.3 64.5 1.0
C1 A:1CX9002 2.3 66.1 1.0
N1 A:1CX9002 2.6 59.2 1.0
OD2 A:ASP208 3.2 60.0 1.0
CE A:LYS97 3.4 66.7 1.0
C4 A:1CX9002 3.5 64.7 1.0
C6 A:1CX9002 3.5 66.9 1.0
CD1 A:ILE141 3.6 66.6 1.0
O1 A:1CX9002 3.6 61.7 1.0
CD A:LYS97 3.6 66.1 1.0
C12 A:1CX9002 3.9 59.4 1.0
CG2 A:ILE141 3.9 66.3 1.0
CE A:MET143 3.9 64.0 1.0
C5 A:1CX9002 4.0 65.7 1.0
CB A:ILE141 4.1 66.7 1.0
SD A:MET143 4.3 64.6 1.0
CG A:ASP208 4.3 57.3 1.0
CG1 A:ILE141 4.4 66.7 1.0
F2 A:1CX9002 4.5 58.5 1.0
C13 A:1CX9002 4.5 62.4 1.0
NZ A:LYS97 4.6 67.7 1.0
CA A:ASP208 4.7 57.0 1.0
N A:ASP208 4.7 57.3 1.0
CB A:LYS97 4.7 64.9 1.0
C7 A:1CX9002 4.7 60.7 1.0
C11 A:1CX9002 4.8 58.3 1.0
CG A:LYS97 4.8 65.3 1.0

Reference:

H.Tecle, J.Shao, Y.Li, M.Kothe, S.Kazmirski, J.Penzotti, Y.H.Ding, J.Ohren, D.Moshinsky, R.Coli, N.Jhawar, E.Bora, S.Jacques-O'hagan, J.Wu. Beyond the Mek-Pocket: Can Current Mek Kinase Inhibitors Be Utilized to Synthesize Novel Type III Nckis? Does the Mek-Pocket Exist in Kinases Other Than Mek? Bioorg.Med.Chem.Lett. V. 19 226 2009.
ISSN: ISSN 0960-894X
PubMed: 19019675
DOI: 10.1016/J.BMCL.2008.10.108
Page generated: Wed Jul 31 18:11:55 2024

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