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Fluorine in PDB 4rzv: Crystal Structure of the Braf (R509H) Kinase Domain Monomer Bound to Vemurafenib

Enzymatic activity of Crystal Structure of the Braf (R509H) Kinase Domain Monomer Bound to Vemurafenib

All present enzymatic activity of Crystal Structure of the Braf (R509H) Kinase Domain Monomer Bound to Vemurafenib:
2.7.11.1;

Protein crystallography data

The structure of Crystal Structure of the Braf (R509H) Kinase Domain Monomer Bound to Vemurafenib, PDB code: 4rzv was solved by Y.Wu, E.Gavathiotis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.77 / 2.99
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 64.975, 71.698, 243.281, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 26.7

Other elements in 4rzv:

The structure of Crystal Structure of the Braf (R509H) Kinase Domain Monomer Bound to Vemurafenib also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the Braf (R509H) Kinase Domain Monomer Bound to Vemurafenib (pdb code 4rzv). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of the Braf (R509H) Kinase Domain Monomer Bound to Vemurafenib, PDB code: 4rzv:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 4rzv

Go back to Fluorine Binding Sites List in 4rzv
Fluorine binding site 1 out of 4 in the Crystal Structure of the Braf (R509H) Kinase Domain Monomer Bound to Vemurafenib


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 Braf (R509H) Kinase Domain Monomer Bound to Vemurafenib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:49.2
occ:1.00
 F25 A:032801 0.0 49.2 1.0
C24 A:032801 1.4 39.8 1.0
C23 A:032801 2.1 39.6 1.0
C18 A:032801 2.6 37.4 1.0
C17 A:032801 3.2 32.4 1.0
CB A:ALA481 3.4 31.7 1.0
CG1 A:VAL471 3.4 36.6 1.0
C22 A:032801 3.5 35.0 1.0
C15 A:032801 3.6 22.7 1.0
C A:ALA481 3.6 29.9 1.0
O A:ALA481 3.6 29.9 1.0
N A:LYS483 3.7 30.8 1.0
C16 A:032801 3.7 26.5 1.0
C20 A:032801 3.7 39.4 1.0
C A:VAL482 3.7 29.6 1.0
OG1 A:THR529 3.8 38.4 1.0
N A:VAL482 3.8 29.1 1.0
CB A:LYS483 3.9 38.8 1.0
O19 A:032801 4.0 30.5 1.0
CB A:VAL471 4.0 39.3 1.0
O A:VAL482 4.1 30.4 1.0
C21 A:032801 4.1 33.1 1.0
CA A:ALA481 4.1 30.7 1.0
CA A:LYS483 4.2 35.4 1.0
CA A:VAL482 4.2 28.9 1.0
O A:ILE527 4.4 36.1 1.0
N14 A:032801 4.6 22.0 1.0
CA A:VAL471 4.7 32.8 1.0
C05 A:032801 4.7 24.2 1.0
F26 A:032801 4.9 44.0 1.0
O A:TYR472 5.0 28.5 1.0
CE A:LYS483 5.0 47.7 1.0

Fluorine binding site 2 out of 4 in 4rzv

Go back to Fluorine Binding Sites List in 4rzv
Fluorine binding site 2 out of 4 in the Crystal Structure of the Braf (R509H) Kinase Domain Monomer Bound to Vemurafenib


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 Braf (R509H) Kinase Domain Monomer Bound to Vemurafenib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:44.0
occ:1.00
 F26 A:032801 0.0 44.0 1.0
C20 A:032801 1.4 39.4 1.0
C18 A:032801 2.4 37.4 1.0
C21 A:032801 2.4 33.1 1.0
N27 A:032801 2.8 29.5 1.0
C17 A:032801 2.8 32.4 1.0
O19 A:032801 3.0 30.5 1.0
N A:ASP594 3.2 30.5 1.0
CE2 A:PHE583 3.3 25.1 1.0
CA A:GLY593 3.5 27.8 1.0
CZ A:PHE583 3.6 26.0 1.0
CD2 A:LEU514 3.6 34.1 1.0
C24 A:032801 3.6 39.8 1.0
C22 A:032801 3.6 35.0 1.0
C A:GLY593 3.7 29.7 1.0
C16 A:032801 3.8 26.5 1.0
C15 A:032801 4.0 22.7 1.0
CA A:ASP594 4.1 36.8 1.0
C23 A:032801 4.1 39.6 1.0
CB A:ASP594 4.3 43.6 1.0
CD2 A:PHE583 4.4 25.1 1.0
S28 A:032801 4.5 43.0 1.0
N A:GLY593 4.6 29.4 1.0
NZ A:LYS483 4.7 48.2 1.0
O A:GLY593 4.8 34.0 1.0
CG A:ASP594 4.8 55.2 1.0
CE1 A:PHE583 4.9 26.9 1.0
F25 A:032801 4.9 49.2 1.0
CE A:LYS483 5.0 47.7 1.0
C05 A:032801 5.0 24.2 1.0
CG A:LEU514 5.0 31.9 1.0

Fluorine binding site 3 out of 4 in 4rzv

Go back to Fluorine Binding Sites List in 4rzv
Fluorine binding site 3 out of 4 in the Crystal Structure of the Braf (R509H) Kinase Domain Monomer Bound to Vemurafenib


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 Braf (R509H) Kinase Domain Monomer Bound to Vemurafenib within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:49.3
occ:1.00
 F25 B:032801 0.0 49.3 1.0
C24 B:032801 1.4 41.9 1.0
C23 B:032801 2.1 41.1 1.0
C18 B:032801 2.6 41.1 1.0
C17 B:032801 3.2 38.9 1.0
C B:ALA481 3.3 36.8 1.0
N B:VAL482 3.4 35.0 1.0
O B:ALA481 3.4 36.0 1.0
CB B:ALA481 3.4 37.0 1.0
C22 B:032801 3.5 42.5 1.0
C B:VAL482 3.5 40.8 1.0
N B:LYS483 3.5 40.7 1.0
OG1 B:THR529 3.6 41.0 1.0
C15 B:032801 3.6 34.7 1.0
CG1 B:VAL471 3.7 41.5 1.0
C16 B:032801 3.7 39.0 1.0
CA B:VAL482 3.7 34.6 1.0
C20 B:032801 3.7 49.1 1.0
O B:VAL482 4.0 39.0 1.0
O19 B:032801 4.0 46.4 1.0
CA B:ALA481 4.0 38.0 1.0
CB B:LYS483 4.1 41.1 1.0
C21 B:032801 4.1 45.4 1.0
O B:ILE527 4.1 37.1 1.0
CA B:LYS483 4.2 49.0 1.0
CG2 B:VAL471 4.4 39.5 1.0
CB B:VAL471 4.5 40.4 1.0
N14 B:032801 4.6 35.4 1.0
C05 B:032801 4.7 41.3 1.0
CB B:THR529 4.8 42.1 1.0
O B:TYR472 4.9 49.4 1.0
CG2 B:THR529 4.9 38.9 1.0
N B:THR529 4.9 39.6 1.0
F26 B:032801 4.9 51.9 1.0

Fluorine binding site 4 out of 4 in 4rzv

Go back to Fluorine Binding Sites List in 4rzv
Fluorine binding site 4 out of 4 in the Crystal Structure of the Braf (R509H) Kinase Domain Monomer Bound to Vemurafenib


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 Braf (R509H) Kinase Domain Monomer Bound to Vemurafenib within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:51.9
occ:1.00
 F26 B:032801 0.0 51.9 1.0
C20 B:032801 1.4 49.1 1.0
C21 B:032801 2.4 45.4 1.0
C18 B:032801 2.4 41.1 1.0
N27 B:032801 2.8 44.5 1.0
C17 B:032801 2.8 38.9 1.0
O19 B:032801 3.1 46.4 1.0
CD2 B:LEU514 3.3 30.4 1.0
CE2 B:PHE583 3.4 37.3 1.0
OD1 B:ASP594 3.5 70.1 1.0
N B:ASP594 3.5 36.0 1.0
CA B:GLY593 3.6 34.0 1.0
C22 B:032801 3.6 42.5 1.0
C24 B:032801 3.6 41.9 1.0
CZ B:PHE583 3.7 39.0 1.0
C16 B:032801 3.8 39.0 1.0
C B:GLY593 3.9 33.7 1.0
C15 B:032801 4.1 34.7 1.0
C23 B:032801 4.1 41.1 1.0
CG B:ASP594 4.1 66.6 1.0
S28 B:032801 4.5 30.6 1.0
CD2 B:PHE583 4.5 36.6 1.0
CA B:ASP594 4.6 43.8 1.0
NZ B:LYS483 4.7 41.6 1.0
N B:GLY593 4.7 31.9 1.0
OD2 B:ASP594 4.8 71.9 1.0
CG B:LEU514 4.8 36.8 1.0
CB B:ASP594 4.8 53.8 1.0
CE B:LYS483 4.9 42.4 1.0
F25 B:032801 4.9 49.3 1.0
C05 B:032801 5.0 41.3 1.0

Reference:

Z.Karoulia, Y.Wu, T.A.Ahmed, X.Qisheng, J.Bollard, C.Krepler, X.Wu, C.Zhang, G.Bollag, M.Herlym, J.A.Fagin, A.Lujambio, E.Gavathiotis, P.I.Poulikakos. An Integrated Model of Raf Inhibitor Action Predicts Inhibitor Activity Against Oncogenic Braf Signaling Cancer Cell V. 30 1 2016.
ISSN: ISSN 1535-6108
Page generated: Sun Dec 13 12:12:22 2020

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