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Fluorine in PDB 5mz3: P38 Alpha Mutant C162S in Complex with CMPD2 [N-(4-Methyl-3-(4,4,5,5- Tetramethyl-1,3,2-Dioxaborolan-2-Yl)Phenyl)-3-(Trifluoromethyl) Benzamide]

Enzymatic activity of P38 Alpha Mutant C162S in Complex with CMPD2 [N-(4-Methyl-3-(4,4,5,5- Tetramethyl-1,3,2-Dioxaborolan-2-Yl)Phenyl)-3-(Trifluoromethyl) Benzamide]

All present enzymatic activity of P38 Alpha Mutant C162S in Complex with CMPD2 [N-(4-Methyl-3-(4,4,5,5- Tetramethyl-1,3,2-Dioxaborolan-2-Yl)Phenyl)-3-(Trifluoromethyl) Benzamide]:
2.7.11.24;

Protein crystallography data

The structure of P38 Alpha Mutant C162S in Complex with CMPD2 [N-(4-Methyl-3-(4,4,5,5- Tetramethyl-1,3,2-Dioxaborolan-2-Yl)Phenyl)-3-(Trifluoromethyl) Benzamide], PDB code: 5mz3 was solved by S.W.Cowan-Jacob, C.Scheufler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.34 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.919, 85.607, 127.468, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 19.7

Fluorine Binding Sites:

The binding sites of Fluorine atom in the P38 Alpha Mutant C162S in Complex with CMPD2 [N-(4-Methyl-3-(4,4,5,5- Tetramethyl-1,3,2-Dioxaborolan-2-Yl)Phenyl)-3-(Trifluoromethyl) Benzamide] (pdb code 5mz3). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the P38 Alpha Mutant C162S in Complex with CMPD2 [N-(4-Methyl-3-(4,4,5,5- Tetramethyl-1,3,2-Dioxaborolan-2-Yl)Phenyl)-3-(Trifluoromethyl) Benzamide], PDB code: 5mz3:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 5mz3

Go back to Fluorine Binding Sites List in 5mz3
Fluorine binding site 1 out of 3 in the P38 Alpha Mutant C162S in Complex with CMPD2 [N-(4-Methyl-3-(4,4,5,5- Tetramethyl-1,3,2-Dioxaborolan-2-Yl)Phenyl)-3-(Trifluoromethyl) Benzamide]


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of P38 Alpha Mutant C162S in Complex with CMPD2 [N-(4-Methyl-3-(4,4,5,5- Tetramethyl-1,3,2-Dioxaborolan-2-Yl)Phenyl)-3-(Trifluoromethyl) Benzamide] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:44.1
occ:1.00
 F31 A:8EN401 0.0 44.1 1.0
C30 A:8EN401 1.4 39.9 1.0
F33 A:8EN401 2.2 40.2 1.0
F32 A:8EN401 2.2 42.2 1.0
C14 A:8EN401 2.4 33.3 1.0
C13 A:8EN401 2.8 34.9 1.0
CD2 A:HIS148 3.7 23.3 1.0
C15 A:8EN401 3.7 30.0 1.0
O A:HOH557 3.9 36.8 1.0
CD2 A:LEU74 4.1 37.2 1.0
C12 A:8EN401 4.2 35.1 1.0
NE2 A:HIS148 4.3 23.4 1.0
O A:HOH747 4.3 52.9 1.0
CG A:HIS148 4.4 23.0 1.0
CD1 A:ILE141 4.5 15.0 1.0
CG A:LEU74 4.8 34.2 1.0
C9 A:8EN401 4.8 30.0 1.0
CB A:HIS148 4.9 20.1 1.0
CA A:HIS148 4.9 19.7 1.0
CG2 A:ILE141 5.0 20.8 1.0
CG2 A:ILE146 5.0 22.6 1.0

Fluorine binding site 2 out of 3 in 5mz3

Go back to Fluorine Binding Sites List in 5mz3
Fluorine binding site 2 out of 3 in the P38 Alpha Mutant C162S in Complex with CMPD2 [N-(4-Methyl-3-(4,4,5,5- Tetramethyl-1,3,2-Dioxaborolan-2-Yl)Phenyl)-3-(Trifluoromethyl) Benzamide]


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of P38 Alpha Mutant C162S in Complex with CMPD2 [N-(4-Methyl-3-(4,4,5,5- Tetramethyl-1,3,2-Dioxaborolan-2-Yl)Phenyl)-3-(Trifluoromethyl) Benzamide] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:42.2
occ:1.00
 F32 A:8EN401 0.0 42.2 1.0
C30 A:8EN401 1.4 39.9 1.0
F33 A:8EN401 2.2 40.2 1.0
F31 A:8EN401 2.2 44.1 1.0
C14 A:8EN401 2.4 33.3 1.0
C15 A:8EN401 2.9 30.0 1.0
C A:LEU167 3.4 25.8 1.0
CD2 A:HIS148 3.5 23.3 1.0
O A:LEU167 3.5 24.0 1.0
C13 A:8EN401 3.5 34.9 1.0
NE2 A:HIS148 3.5 23.4 1.0
CA A:LEU167 3.6 23.5 1.0
CG2 A:ILE166 3.8 19.8 1.0
N A:ASP168 3.9 24.2 1.0
N A:LEU167 3.9 22.2 1.0
O A:ILE166 3.9 23.1 1.0
C A:ILE166 4.0 24.5 1.0
C9 A:8EN401 4.2 30.0 1.0
CB A:ASP168 4.3 26.7 1.0
CG2 A:ILE84 4.3 27.3 1.0
CA A:ASP168 4.6 25.0 1.0
CG1 A:VAL83 4.7 19.9 1.0
C12 A:8EN401 4.7 35.1 1.0
CG A:HIS148 4.7 23.0 1.0
CD1 A:ILE141 4.7 15.0 1.0
CE1 A:HIS148 4.8 23.7 1.0
CB A:ILE166 4.8 19.8 1.0
O A:HOH557 4.8 36.8 1.0
O10 A:8EN401 4.9 29.6 1.0
C11 A:8EN401 5.0 32.8 1.0

Fluorine binding site 3 out of 3 in 5mz3

Go back to Fluorine Binding Sites List in 5mz3
Fluorine binding site 3 out of 3 in the P38 Alpha Mutant C162S in Complex with CMPD2 [N-(4-Methyl-3-(4,4,5,5- Tetramethyl-1,3,2-Dioxaborolan-2-Yl)Phenyl)-3-(Trifluoromethyl) Benzamide]


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of P38 Alpha Mutant C162S in Complex with CMPD2 [N-(4-Methyl-3-(4,4,5,5- Tetramethyl-1,3,2-Dioxaborolan-2-Yl)Phenyl)-3-(Trifluoromethyl) Benzamide] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:40.2
occ:1.00
 F33 A:8EN401 0.0 40.2 1.0
C30 A:8EN401 1.3 39.9 1.0
F32 A:8EN401 2.2 42.2 1.0
F31 A:8EN401 2.2 44.1 1.0
C14 A:8EN401 2.4 33.3 1.0
C15 A:8EN401 3.1 30.0 1.0
C13 A:8EN401 3.4 34.9 1.0
CG1 A:VAL83 3.6 19.9 1.0
CG2 A:ILE84 3.9 27.3 1.0
CG A:MET78 4.1 32.9 1.0
C9 A:8EN401 4.4 30.0 1.0
C12 A:8EN401 4.6 35.1 1.0
CD1 A:ILE141 4.6 15.0 1.0
SD A:MET78 4.6 38.5 1.0
O A:ILE166 4.7 23.1 1.0
CD2 A:LEU74 4.7 37.2 1.0
CG A:LEU74 4.8 34.2 1.0

Reference:

A.Smith, Z.J.Ni, D.Poon, Z.Huang, Z.Chen, Q.Zhang, L.Tandeske, H.Merritt, K.Shoemaker, J.Chan, S.Kaufman, K.Huh, J.Murray, B.A.Appleton, S.W.Cowan-Jacob, C.Scheufler, T.Kanazawa, J.M.Jansen, D.Stuart, C.M.Shafer. Imidazo[1,2-A]Pyridin-6-Yl-Benzamide Analogs As Potent Raf Inhibitors. Bioorg. Med. Chem. Lett. V. 27 5221 2017.
ISSN: ESSN 1464-3405
PubMed: 29107542
DOI: 10.1016/J.BMCL.2017.10.047
Page generated: Tue Jul 15 05:24:29 2025

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