Atomistry » Fluorine » PDB 5msb-5njh » 5mz3
Atomistry »
  Fluorine »
    PDB 5msb-5njh »
      5mz3 »

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: Thu Aug 1 11:53:29 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy