Fluorine in PDB 7jxp: Egfr Kinase (T790M/V948R) in Complex with Osimertinib and Jbj-04-125- 02

Enzymatic activity of Egfr Kinase (T790M/V948R) in Complex with Osimertinib and Jbj-04-125- 02

All present enzymatic activity of Egfr Kinase (T790M/V948R) in Complex with Osimertinib and Jbj-04-125- 02:
2.7.10.1;

Protein crystallography data

The structure of Egfr Kinase (T790M/V948R) in Complex with Osimertinib and Jbj-04-125- 02, PDB code: 7jxp was solved by T.S.Beyett, M.J.Eck, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 89.11 / 2.16
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 57.113, 94.741, 95.569, 70.56, 78.4, 79.18
R / Rfree (%) 21.2 / 24.7

Other elements in 7jxp:

The structure of Egfr Kinase (T790M/V948R) in Complex with Osimertinib and Jbj-04-125- 02 also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Egfr Kinase (T790M/V948R) in Complex with Osimertinib and Jbj-04-125- 02 (pdb code 7jxp). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Egfr Kinase (T790M/V948R) in Complex with Osimertinib and Jbj-04-125- 02, PDB code: 7jxp:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 7jxp

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Fluorine binding site 1 out of 6 in the Egfr Kinase (T790M/V948R) in Complex with Osimertinib and Jbj-04-125- 02


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Egfr Kinase (T790M/V948R) in Complex with Osimertinib and Jbj-04-125- 02 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F1103

b:36.2
occ:1.00
 F35 D:JBJ1103 0.0 36.2 1.0
C34 D:JBJ1103 1.4 31.9 1.0
C33 D:JBJ1103 2.3 32.1 1.0
C36 D:JBJ1103 2.4 36.3 1.0
N D:LEU777 3.1 35.3 1.0
C D:ARG776 3.1 34.9 1.0
O D:ARG776 3.2 33.0 1.0
CA D:LEU777 3.4 37.3 1.0
CE D:MET790 3.5 27.5 1.0
C32 D:JBJ1103 3.6 32.5 1.0
C37 D:JBJ1103 3.6 35.8 1.0
C D:CYS775 3.8 32.5 1.0
N D:ARG776 3.8 30.5 1.0
O D:CYS775 3.8 35.0 1.0
CB D:CYS775 3.9 31.5 1.0
CA D:ARG776 3.9 31.7 1.0
SD D:MET790 4.0 38.0 1.0
CB D:LEU777 4.0 37.1 1.0
C38 D:JBJ1103 4.1 34.8 1.0
CB D:MET790 4.1 32.9 1.0
OG1 D:THR854 4.2 32.3 1.0
CA D:CYS775 4.5 30.1 1.0
CD1 D:LEU777 4.7 32.9 1.0
CG D:MET790 4.7 31.2 1.0
C02 D:JBJ1103 4.8 34.9 1.0
C D:LEU777 4.8 34.5 1.0
C09 D:JBJ1103 4.8 34.1 1.0
O D:HOH1234 4.9 31.1 1.0
CG D:LEU777 5.0 37.9 1.0

Fluorine binding site 2 out of 6 in 7jxp

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Fluorine binding site 2 out of 6 in the Egfr Kinase (T790M/V948R) in Complex with Osimertinib and Jbj-04-125- 02


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Egfr Kinase (T790M/V948R) in Complex with Osimertinib and Jbj-04-125- 02 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1103

b:35.1
occ:1.00
 F35 A:JBJ1103 0.0 35.1 1.0
C34 A:JBJ1103 1.4 33.5 1.0
C36 A:JBJ1103 2.4 35.6 1.0
C33 A:JBJ1103 2.4 31.6 1.0
O A:ARG776 3.0 33.0 1.0
C A:ARG776 3.0 32.3 1.0
N A:LEU777 3.0 30.8 1.0
CA A:LEU777 3.4 32.4 1.0
C37 A:JBJ1103 3.6 35.6 1.0
C32 A:JBJ1103 3.7 35.0 1.0
N A:ARG776 3.7 33.4 1.0
C A:CYS775 3.7 35.3 1.0
CE A:MET790 3.7 25.8 1.0
CA A:ARG776 3.8 32.3 1.0
O A:CYS775 3.8 34.1 1.0
CB A:CYS775 3.9 33.9 1.0
CB A:LEU777 3.9 34.0 1.0
SD A:MET790 4.1 36.7 1.0
C38 A:JBJ1103 4.1 32.2 1.0
CB A:MET790 4.1 30.3 1.0
OG1 A:THR854 4.4 34.8 1.0
CA A:CYS775 4.5 33.7 1.0
CD1 A:LEU777 4.6 30.9 1.0
C A:LEU777 4.7 35.4 1.0
O A:HOH1246 4.7 29.8 1.0
CG A:MET790 4.8 30.6 1.0
C02 A:JBJ1103 4.9 33.6 1.0
C09 A:JBJ1103 4.9 34.2 1.0
CG A:LEU777 5.0 35.4 1.0

Fluorine binding site 3 out of 6 in 7jxp

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Fluorine binding site 3 out of 6 in the Egfr Kinase (T790M/V948R) in Complex with Osimertinib and Jbj-04-125- 02


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Egfr Kinase (T790M/V948R) in Complex with Osimertinib and Jbj-04-125- 02 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1101

b:37.0
occ:1.00
 F35 C:JBJ1101 0.0 37.0 1.0
C34 C:JBJ1101 1.4 42.3 1.0
C33 C:JBJ1101 2.4 41.0 1.0
C36 C:JBJ1101 2.4 45.7 1.0
C C:ARG776 2.9 41.9 1.0
O C:ARG776 3.0 41.0 1.0
N C:LEU777 3.0 40.7 1.0
CA C:LEU777 3.5 42.5 1.0
CE C:MET790 3.5 40.2 1.0
C37 C:JBJ1101 3.6 45.5 1.0
N C:ARG776 3.6 37.4 1.0
C32 C:JBJ1101 3.6 42.2 1.0
C C:CYS775 3.7 39.7 1.0
CA C:ARG776 3.7 40.8 1.0
O C:CYS775 3.8 39.1 1.0
CB C:CYS775 3.9 38.8 1.0
CB C:LEU777 4.0 45.1 1.0
SD C:MET790 4.0 40.7 1.0
C38 C:JBJ1101 4.1 45.4 1.0
CB C:MET790 4.2 40.2 1.0
OG1 C:THR854 4.3 46.2 1.0
CA C:CYS775 4.4 35.5 1.0
CG C:MET790 4.8 42.8 1.0
CD1 C:LEU777 4.8 48.3 1.0
C02 C:JBJ1101 4.8 42.2 1.0
C C:LEU777 4.8 42.4 1.0
O C:MET766 4.8 48.9 0.5
C09 C:JBJ1101 4.9 43.9 1.0
O C:HOH1218 5.0 29.0 1.0
O C:MET766 5.0 49.1 0.5

Fluorine binding site 4 out of 6 in 7jxp

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Fluorine binding site 4 out of 6 in the Egfr Kinase (T790M/V948R) in Complex with Osimertinib and Jbj-04-125- 02


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Egfr Kinase (T790M/V948R) in Complex with Osimertinib and Jbj-04-125- 02 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F1103

b:30.7
occ:1.00
 F35 F:JBJ1103 0.0 30.7 1.0
C34 F:JBJ1103 1.4 34.6 1.0
C33 F:JBJ1103 2.4 32.3 1.0
C36 F:JBJ1103 2.4 35.9 1.0
C F:ARG776 3.1 34.9 1.0
N F:LEU777 3.1 33.4 1.0
O F:ARG776 3.1 30.5 1.0
CA F:LEU777 3.4 36.0 1.0
CE F:MET790 3.6 37.5 1.0
C37 F:JBJ1103 3.6 37.2 1.0
C32 F:JBJ1103 3.6 35.0 1.0
C F:CYS775 3.8 36.5 1.0
O F:CYS775 3.8 37.2 1.0
N F:ARG776 3.8 38.5 1.0
CA F:ARG776 3.8 35.9 1.0
CB F:CYS775 3.9 37.5 1.0
CB F:LEU777 4.0 36.1 1.0
SD F:MET790 4.0 42.0 1.0
C38 F:JBJ1103 4.1 34.4 1.0
CB F:MET790 4.2 34.4 1.0
OG1 F:THR854 4.3 40.5 1.0
CA F:CYS775 4.5 38.6 1.0
CG F:MET790 4.7 37.6 1.0
C F:LEU777 4.8 32.0 1.0
C02 F:JBJ1103 4.8 37.3 1.0
O F:HOH1222 4.9 33.7 1.0
C09 F:JBJ1103 4.9 35.0 1.0
CD1 F:LEU777 4.9 35.5 1.0

Fluorine binding site 5 out of 6 in 7jxp

Go back to Fluorine Binding Sites List in 7jxp
Fluorine binding site 5 out of 6 in the Egfr Kinase (T790M/V948R) in Complex with Osimertinib and Jbj-04-125- 02


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Egfr Kinase (T790M/V948R) in Complex with Osimertinib and Jbj-04-125- 02 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1103

b:30.1
occ:1.00
 F35 B:JBJ1103 0.0 30.1 1.0
C34 B:JBJ1103 1.4 29.8 1.0
C36 B:JBJ1103 2.4 34.2 1.0
C33 B:JBJ1103 2.4 31.8 1.0
N B:LEU777 3.1 32.2 1.0
C B:ARG776 3.2 32.4 1.0
O B:ARG776 3.2 34.7 1.0
CA B:LEU777 3.4 35.9 1.0
CE B:MET790 3.4 30.4 1.0
C37 B:JBJ1103 3.6 33.5 1.0
C32 B:JBJ1103 3.7 32.6 1.0
O B:CYS775 3.8 34.7 1.0
C B:CYS775 3.8 37.0 1.0
CB B:CYS775 3.9 36.0 1.0
N B:ARG776 3.9 35.3 1.0
CB B:LEU777 3.9 35.4 1.0
SD B:MET790 3.9 42.1 1.0
CA B:ARG776 4.0 34.4 1.0
C38 B:JBJ1103 4.1 33.9 1.0
CB B:MET790 4.2 32.9 1.0
OG1 B:THR854 4.3 34.9 1.0
CA B:CYS775 4.5 35.7 1.0
CD1 B:LEU777 4.7 33.6 1.0
CG B:MET790 4.7 34.4 1.0
C02 B:JBJ1103 4.8 36.1 1.0
C B:LEU777 4.8 35.5 1.0
O B:HOH1221 4.9 34.6 1.0
C09 B:JBJ1103 4.9 35.1 1.0
CG B:LEU777 4.9 37.4 1.0
O01 B:JBJ1103 5.0 38.1 1.0

Fluorine binding site 6 out of 6 in 7jxp

Go back to Fluorine Binding Sites List in 7jxp
Fluorine binding site 6 out of 6 in the Egfr Kinase (T790M/V948R) in Complex with Osimertinib and Jbj-04-125- 02


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Egfr Kinase (T790M/V948R) in Complex with Osimertinib and Jbj-04-125- 02 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F1101

b:46.5
occ:1.00
 F35 E:JBJ1101 0.0 46.5 1.0
C34 E:JBJ1101 1.4 48.6 1.0
C33 E:JBJ1101 2.3 51.5 1.0
C36 E:JBJ1101 2.4 53.4 1.0
N E:LEU777 3.0 45.5 1.0
C E:ARG776 3.1 43.6 1.0
O E:ARG776 3.3 43.0 1.0
CA E:LEU777 3.4 46.9 1.0
C32 E:JBJ1101 3.6 55.4 1.0
C37 E:JBJ1101 3.6 51.6 1.0
CE E:MET790 3.7 48.2 1.0
CB E:LEU777 3.8 49.6 1.0
N E:ARG776 3.9 50.6 1.0
CA E:ARG776 3.9 43.2 1.0
O E:CYS775 3.9 45.1 1.0
C E:CYS775 3.9 47.9 1.0
SD E:MET790 4.0 50.0 1.0
C38 E:JBJ1101 4.1 52.5 1.0
CB E:CYS775 4.1 48.4 1.0
CB E:MET790 4.2 46.4 1.0
OG1 E:THR854 4.6 52.1 1.0
CD1 E:LEU777 4.6 52.7 1.0
CA E:CYS775 4.7 45.6 1.0
CG E:MET790 4.7 51.1 1.0
C02 E:JBJ1101 4.7 56.5 1.0
C E:LEU777 4.8 48.3 1.0
C09 E:JBJ1101 4.8 59.1 1.0
CG E:LEU777 4.9 51.9 1.0
O01 E:JBJ1101 4.9 56.8 1.0
O E:MET766 5.0 48.5 1.0

Reference:

T.S.Beyett, C.To, D.E.Heppner, J.Jang, B.H.Shin, G.Gomez, P.A.Janne, N.S.Gray, M.J.Eck. Egfr (T790M/V948R) Kinase in Complex with Osimertinib and Jbj-04-125-02 To Be Published.
Page generated: Fri Aug 2 08:05:04 2024

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