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Fluorine in PDB 5g4o: Crystal Structure of the P53 Cancer Mutant Y220C in Complex with A Trifluorinated Derivative of the Small Molecule Stabilizer PHIKAN083

Protein crystallography data

The structure of Crystal Structure of the P53 Cancer Mutant Y220C in Complex with A Trifluorinated Derivative of the Small Molecule Stabilizer PHIKAN083, PDB code: 5g4o was solved by A.C.Joerger, M.Bauer, M.G.J.Baud, J.Spencer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.53 / 1.48
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.162, 71.448, 105.235, 90.00, 90.00, 90.00
R / Rfree (%) 14.4 / 17.1

Other elements in 5g4o:

The structure of Crystal Structure of the P53 Cancer Mutant Y220C in Complex with A Trifluorinated Derivative of the Small Molecule Stabilizer PHIKAN083 also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the P53 Cancer Mutant Y220C in Complex with A Trifluorinated Derivative of the Small Molecule Stabilizer PHIKAN083 (pdb code 5g4o). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of the P53 Cancer Mutant Y220C in Complex with A Trifluorinated Derivative of the Small Molecule Stabilizer PHIKAN083, PDB code: 5g4o:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5g4o

Go back to Fluorine Binding Sites List in 5g4o
Fluorine binding site 1 out of 6 in the Crystal Structure of the P53 Cancer Mutant Y220C in Complex with A Trifluorinated Derivative of the Small Molecule Stabilizer PHIKAN083


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 the P53 Cancer Mutant Y220C in Complex with A Trifluorinated Derivative of the Small Molecule Stabilizer PHIKAN083 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1293

b:25.0
occ:1.00
F1 A:O801293 0.0 25.0 1.0
C14 A:O801293 1.3 26.0 1.0
F2 A:O801293 2.2 24.5 1.0
F3 A:O801293 2.2 26.3 1.0
C13 A:O801293 2.4 27.8 1.0
N1 A:O801293 3.0 29.4 1.0
C9 A:O801293 3.1 29.2 1.0
C4 A:O801293 3.3 28.5 1.0
CG1 A:VAL147 3.3 15.1 1.0
O A:LEU145 3.5 13.6 1.0
C A:LEU145 3.6 12.3 1.0
CG2 A:VAL147 3.6 15.3 1.0
CB A:LEU145 3.6 12.9 1.0
C A:TRP146 3.7 12.7 1.0
N A:TRP146 3.8 11.0 1.0
N A:VAL147 3.8 13.7 1.0
CB A:VAL147 3.9 14.0 1.0
O A:TRP146 4.0 13.3 1.0
CA A:TRP146 4.1 11.8 1.0
C1 A:O801293 4.2 30.3 1.0
CA A:LEU145 4.2 11.5 1.0
C10 A:O801293 4.3 30.6 1.0
OG1 A:THR230 4.4 17.3 0.4
CA A:VAL147 4.4 14.3 1.0
C3 A:O801293 4.5 29.6 1.0
CD1 A:PHE109 4.5 13.2 1.0
CE1 A:PHE109 4.7 14.9 1.0
SG A:CYS220 4.7 25.2 0.7
CG A:LEU145 4.9 13.4 1.0
C2 A:O801293 4.9 30.9 1.0
CD1 A:LEU145 4.9 17.2 1.0
C5 A:O801293 5.0 32.4 1.0

Fluorine binding site 2 out of 6 in 5g4o

Go back to Fluorine Binding Sites List in 5g4o
Fluorine binding site 2 out of 6 in the Crystal Structure of the P53 Cancer Mutant Y220C in Complex with A Trifluorinated Derivative of the Small Molecule Stabilizer PHIKAN083


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 the P53 Cancer Mutant Y220C in Complex with A Trifluorinated Derivative of the Small Molecule Stabilizer PHIKAN083 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1293

b:24.5
occ:1.00
F2 A:O801293 0.0 24.5 1.0
C14 A:O801293 1.3 26.0 1.0
F1 A:O801293 2.2 25.0 1.0
F3 A:O801293 2.2 26.3 1.0
C13 A:O801293 2.3 27.8 1.0
SG A:CYS220 3.2 25.2 0.7
CB A:LEU145 3.3 12.9 1.0
CD1 A:LEU145 3.4 17.2 1.0
N1 A:O801293 3.6 29.4 1.0
CG A:LEU145 4.0 13.4 1.0
OG1 A:THR230 4.0 17.3 0.4
CE1 A:PHE109 4.2 14.9 1.0
CD1 A:LEU257 4.2 14.7 1.0
CG2 A:VAL157 4.2 14.1 0.7
SG A:CYS220 4.4 27.0 0.3
C1 A:O801293 4.5 30.3 1.0
CD1 A:PHE109 4.5 13.2 1.0
C4 A:O801293 4.5 28.5 1.0
CA A:LEU145 4.5 11.5 1.0
C A:LEU145 4.6 12.3 1.0
CB A:CYS220 4.6 21.9 0.7
C5 A:O801293 4.7 32.4 1.0
CG1 A:VAL147 4.7 15.1 1.0
O A:LEU145 4.7 13.6 1.0
C9 A:O801293 4.7 29.2 1.0
CD2 A:LEU145 4.8 13.9 1.0
CB A:CYS220 4.9 24.7 0.3

Fluorine binding site 3 out of 6 in 5g4o

Go back to Fluorine Binding Sites List in 5g4o
Fluorine binding site 3 out of 6 in the Crystal Structure of the P53 Cancer Mutant Y220C in Complex with A Trifluorinated Derivative of the Small Molecule Stabilizer PHIKAN083


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 the P53 Cancer Mutant Y220C in Complex with A Trifluorinated Derivative of the Small Molecule Stabilizer PHIKAN083 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1293

b:26.3
occ:1.00
F3 A:O801293 0.0 26.3 1.0
C14 A:O801293 1.3 26.0 1.0
F2 A:O801293 2.2 24.5 1.0
F1 A:O801293 2.2 25.0 1.0
C13 A:O801293 2.3 27.8 1.0
N1 A:O801293 2.7 29.4 1.0
SG A:CYS220 3.0 25.2 0.7
C1 A:O801293 3.2 30.3 1.0
C5 A:O801293 3.5 32.4 1.0
CG1 A:VAL147 3.5 15.1 1.0
C4 A:O801293 3.6 28.5 1.0
CG A:PRO151 3.8 17.8 1.0
CG2 A:VAL147 3.8 15.3 1.0
CD A:PRO151 4.0 17.4 1.0
C2 A:O801293 4.2 30.9 1.0
C9 A:O801293 4.2 29.2 1.0
CB A:VAL147 4.3 14.0 1.0
CD1 A:LEU257 4.3 14.7 1.0
C3 A:O801293 4.4 29.6 1.0
C6 A:O801293 4.6 32.4 1.0
SG A:CYS220 4.7 27.0 0.3
CB A:CYS220 4.8 21.9 0.7
CB A:CYS220 4.8 24.7 0.3
CD2 A:LEU257 4.9 14.8 1.0
CB A:PRO151 5.0 16.5 1.0

Fluorine binding site 4 out of 6 in 5g4o

Go back to Fluorine Binding Sites List in 5g4o
Fluorine binding site 4 out of 6 in the Crystal Structure of the P53 Cancer Mutant Y220C in Complex with A Trifluorinated Derivative of the Small Molecule Stabilizer PHIKAN083


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of the P53 Cancer Mutant Y220C in Complex with A Trifluorinated Derivative of the Small Molecule Stabilizer PHIKAN083 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1292

b:23.4
occ:1.00
F1 B:O801292 0.0 23.4 1.0
C14 B:O801292 1.3 24.1 1.0
F3 B:O801292 2.2 22.4 1.0
F2 B:O801292 2.2 24.3 1.0
C13 B:O801292 2.4 26.8 1.0
N1 B:O801292 3.0 29.6 1.0
C9 B:O801292 3.2 32.4 1.0
C4 B:O801292 3.3 31.2 1.0
CG1 B:VAL147 3.3 18.3 1.0
O B:LEU145 3.4 14.5 1.0
C B:LEU145 3.5 13.2 1.0
CG2 B:VAL147 3.5 16.6 1.0
C B:TRP146 3.6 14.7 1.0
CB B:LEU145 3.6 13.2 1.0
N B:TRP146 3.6 13.1 1.0
N B:VAL147 3.7 15.3 1.0
O B:TRP146 3.9 14.8 1.0
CB B:VAL147 3.9 16.4 1.0
CA B:TRP146 3.9 13.2 1.0
C1 B:O801292 4.1 31.1 1.0
CA B:LEU145 4.1 12.6 1.0
CA B:VAL147 4.4 15.6 1.0
C10 B:O801292 4.4 34.2 1.0
CD1 B:PHE109 4.4 15.1 1.0
C3 B:O801292 4.5 32.6 1.0
CE1 B:PHE109 4.6 16.0 1.0
SG B:CYS220 4.7 26.8 0.4
SG B:CYS220 4.9 22.9 0.6
C5 B:O801292 4.9 31.9 1.0
C2 B:O801292 4.9 32.0 1.0
CG B:LEU145 4.9 14.3 1.0

Fluorine binding site 5 out of 6 in 5g4o

Go back to Fluorine Binding Sites List in 5g4o
Fluorine binding site 5 out of 6 in the Crystal Structure of the P53 Cancer Mutant Y220C in Complex with A Trifluorinated Derivative of the Small Molecule Stabilizer PHIKAN083


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of the P53 Cancer Mutant Y220C in Complex with A Trifluorinated Derivative of the Small Molecule Stabilizer PHIKAN083 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1292

b:24.3
occ:1.00
F2 B:O801292 0.0 24.3 1.0
C14 B:O801292 1.4 24.1 1.0
F1 B:O801292 2.2 23.4 1.0
F3 B:O801292 2.2 22.4 1.0
C13 B:O801292 2.3 26.8 1.0
SG B:CYS220 2.7 26.8 0.4
CB B:LEU145 3.2 13.2 1.0
SG B:CYS220 3.2 22.9 0.6
CD1 B:LEU145 3.5 16.5 1.0
N1 B:O801292 3.6 29.6 1.0
CG B:LEU145 4.0 14.3 1.0
CD1 B:LEU257 4.1 15.1 1.0
CE1 B:PHE109 4.2 16.0 1.0
CG2 B:VAL157 4.4 13.6 0.6
C1 B:O801292 4.4 31.1 1.0
CA B:LEU145 4.4 12.6 1.0
CB B:CYS220 4.5 24.5 0.4
CD1 B:PHE109 4.5 15.1 1.0
C B:LEU145 4.5 13.2 1.0
C4 B:O801292 4.5 31.2 1.0
O B:LEU145 4.6 14.5 1.0
C5 B:O801292 4.6 31.9 1.0
CG1 B:VAL147 4.7 18.3 1.0
CB B:CYS220 4.7 20.9 0.6
CD2 B:LEU145 4.8 15.1 1.0
C9 B:O801292 4.8 32.4 1.0
CB B:THR230 4.9 18.1 1.0

Fluorine binding site 6 out of 6 in 5g4o

Go back to Fluorine Binding Sites List in 5g4o
Fluorine binding site 6 out of 6 in the Crystal Structure of the P53 Cancer Mutant Y220C in Complex with A Trifluorinated Derivative of the Small Molecule Stabilizer PHIKAN083


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of the P53 Cancer Mutant Y220C in Complex with A Trifluorinated Derivative of the Small Molecule Stabilizer PHIKAN083 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1292

b:22.4
occ:1.00
F3 B:O801292 0.0 22.4 1.0
C14 B:O801292 1.3 24.1 1.0
F1 B:O801292 2.2 23.4 1.0
F2 B:O801292 2.2 24.3 1.0
C13 B:O801292 2.4 26.8 1.0
N1 B:O801292 2.7 29.6 1.0
C1 B:O801292 3.1 31.1 1.0
SG B:CYS220 3.2 22.9 0.6
C5 B:O801292 3.4 31.9 1.0
CG1 B:VAL147 3.4 18.3 1.0
SG B:CYS220 3.5 26.8 0.4
C4 B:O801292 3.6 31.2 1.0
CG2 B:VAL147 3.7 16.6 1.0
CG B:PRO151 3.7 19.7 1.0
CD B:PRO151 3.9 19.1 1.0
C2 B:O801292 4.1 32.0 1.0
CB B:VAL147 4.2 16.4 1.0
C9 B:O801292 4.3 32.4 1.0
C3 B:O801292 4.3 32.6 1.0
CD1 B:LEU257 4.4 15.1 1.0
C6 B:O801292 4.5 33.3 1.0
CB B:PRO151 4.9 18.2 1.0
CD2 B:LEU257 4.9 15.6 1.0
CB B:CYS220 5.0 24.5 0.4
CB B:CYS220 5.0 20.9 0.6

Reference:

M.R.Bauer, R.N.Jones, M.G.J.Baud, R.Wilcken, F.M.Boeckler, A.R.Fersht, A.C.Joerger, J.Spencer. Harnessing Fluorine-Sulfur Contacts and Multipolar Interactions For the Design of P53 Mutant Y220C Rescue Drugs. Acs Chem.Biol. V. 11 2265 2016.
ISSN: ISSN 1554-8929
PubMed: 27267810
DOI: 10.1021/ACSCHEMBIO.6B00315
Page generated: Sun Dec 13 12:22:59 2020

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