Atomistry » Fluorine » PDB 5j8m-5jw1 » 5jt2
Atomistry »
  Fluorine »
    PDB 5j8m-5jw1 »
      5jt2 »

Fluorine in PDB 5jt2: BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-Bisamide

Enzymatic activity of BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-Bisamide

All present enzymatic activity of BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-Bisamide:
2.7.11.1;

Protein crystallography data

The structure of BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-Bisamide, PDB code: 5jt2 was solved by M.J.Grasso, R.Marmorstein, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.59 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.102, 68.442, 275.603, 90.00, 90.00, 90.00
R / Rfree (%) 21.2 / 27.3

Fluorine Binding Sites:

The binding sites of Fluorine atom in the BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-Bisamide (pdb code 5jt2). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-Bisamide, PDB code: 5jt2:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 5jt2

Go back to Fluorine Binding Sites List in 5jt2
Fluorine binding site 1 out of 8 in the BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-Bisamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-Bisamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F802

b:21.4
occ:1.00
 F14 A:6NC802 0.0 21.4 1.0
C13 A:6NC802 1.3 20.9 1.0
C12 A:6NC802 2.4 22.1 1.0
C08 A:6NC802 2.4 21.8 1.0
H051 A:6NC802 2.5 30.8 1.0
N05 A:6NC802 2.7 25.7 1.0
C16 A:6NC802 2.7 22.6 1.0
O18 A:6NC802 2.9 20.0 1.0
CE1 B:PHE583 3.2 21.0 1.0
CD1 B:LEU514 3.4 20.7 1.0
CA B:GLY593 3.5 14.9 1.0
C11 A:6NC802 3.6 23.1 1.0
N B:ASP594 3.6 21.5 1.0
C09 A:6NC802 3.6 23.2 1.0
OD2 B:ASP594 3.7 24.0 1.0
CZ B:PHE583 3.7 20.5 1.0
C17 A:6NC802 3.8 22.6 1.0
C B:GLY593 3.9 22.2 1.0
H221 A:6NC802 4.0 29.2 1.0
C10 A:6NC802 4.1 22.6 1.0
C22 A:6NC802 4.2 24.3 1.0
CD1 B:PHE583 4.3 24.6 1.0
H091 A:6NC802 4.4 27.8 1.0
S04 A:6NC802 4.4 24.5 1.0
H032 A:6NC802 4.4 22.7 1.0
N B:GLY593 4.6 16.9 1.0
CG B:ASP594 4.6 30.8 1.0
NZ B:LYS483 4.7 25.1 1.0
CA B:ASP594 4.7 19.6 1.0
F15 A:6NC802 4.7 26.8 1.0
CG B:LEU514 4.8 26.6 1.0
CB B:ASN581 4.9 24.3 1.0
C19 A:6NC802 4.9 23.0 1.0
CE2 B:PHE583 5.0 26.0 1.0

Fluorine binding site 2 out of 8 in 5jt2

Go back to Fluorine Binding Sites List in 5jt2
Fluorine binding site 2 out of 8 in the BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-Bisamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-Bisamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F802

b:26.8
occ:1.00
 F15 A:6NC802 0.0 26.8 1.0
C11 A:6NC802 1.3 23.1 1.0
C10 A:6NC802 2.3 22.6 1.0
C12 A:6NC802 2.4 22.1 1.0
H101 A:6NC802 2.5 27.1 1.0
C16 A:6NC802 3.0 22.6 1.0
H221 A:6NC802 3.2 29.2 1.0
C17 A:6NC802 3.4 22.6 1.0
CB B:ALA481 3.4 23.9 1.0
C22 A:6NC802 3.4 24.3 1.0
C09 A:6NC802 3.6 23.2 1.0
C13 A:6NC802 3.6 20.9 1.0
N B:LYS483 3.7 31.1 1.0
CG1 B:VAL471 3.7 21.9 1.0
C B:ALA481 3.8 25.8 1.0
O18 A:6NC802 3.8 20.0 1.0
N B:VAL482 3.8 25.8 1.0
CG2 B:VAL471 3.8 27.5 1.0
C B:VAL482 3.9 25.6 1.0
CB B:LYS483 4.0 30.2 1.0
O B:ALA481 4.0 26.3 1.0
C08 A:6NC802 4.1 21.8 1.0
CA B:VAL482 4.2 22.8 1.0
CA B:ALA481 4.2 22.9 1.0
OG1 B:THR529 4.3 28.7 1.0
CA B:LYS483 4.3 30.8 1.0
H091 A:6NC802 4.3 27.8 1.0
CB B:VAL471 4.3 28.0 1.0
O B:VAL482 4.4 29.1 1.0
C19 A:6NC802 4.5 23.0 1.0
N21 A:6NC802 4.5 30.7 1.0
O B:ILE527 4.5 24.5 1.0
F14 A:6NC802 4.7 21.4 1.0
CA B:VAL471 5.0 29.6 1.0
C20 A:6NC802 5.0 26.3 1.0

Fluorine binding site 3 out of 8 in 5jt2

Go back to Fluorine Binding Sites List in 5jt2
Fluorine binding site 3 out of 8 in the BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-Bisamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-Bisamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F802

b:20.9
occ:1.00
 F55 A:6NC802 0.0 20.9 1.0
C54 A:6NC802 1.4 23.1 1.0
H461 A:6NC802 2.3 37.5 1.0
C49 A:6NC802 2.4 28.3 1.0
C53 A:6NC802 2.4 25.9 1.0
N46 A:6NC802 2.7 31.2 1.0
C57 A:6NC802 2.8 29.2 1.0
O59 A:6NC802 3.2 26.9 1.0
CE1 A:PHE583 3.2 26.6 1.0
CD1 A:LEU514 3.3 18.2 1.0
OD2 A:ASP594 3.5 42.5 1.0
CA A:GLY593 3.5 23.9 1.0
N A:ASP594 3.6 25.8 1.0
C50 A:6NC802 3.6 27.9 1.0
C52 A:6NC802 3.6 23.2 1.0
CZ A:PHE583 3.8 23.6 1.0
C58 A:6NC802 3.8 24.5 1.0
C A:GLY593 3.9 25.7 1.0
H631 A:6NC802 4.1 27.0 1.0
CD1 A:PHE583 4.1 29.2 1.0
C51 A:6NC802 4.1 29.8 1.0
C63 A:6NC802 4.3 22.5 1.0
S45 A:6NC802 4.3 30.3 1.0
H501 A:6NC802 4.4 33.5 1.0
CG A:ASP594 4.5 42.4 1.0
N A:GLY593 4.6 23.3 1.0
CA A:ASP594 4.7 29.9 1.0
CG A:LEU514 4.7 25.0 1.0
F56 A:6NC802 4.8 23.2 1.0
O A:GLY593 5.0 21.5 1.0
C60 A:6NC802 5.0 25.4 1.0
CB A:ASP594 5.0 32.5 1.0

Fluorine binding site 4 out of 8 in 5jt2

Go back to Fluorine Binding Sites List in 5jt2
Fluorine binding site 4 out of 8 in the BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-Bisamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-Bisamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F802

b:23.2
occ:1.00
 F56 A:6NC802 0.0 23.2 1.0
C52 A:6NC802 1.4 23.2 1.0
C53 A:6NC802 2.4 25.9 1.0
C51 A:6NC802 2.4 29.8 1.0
H511 A:6NC802 2.6 35.7 1.0
C57 A:6NC802 2.8 29.2 1.0
CB A:ALA481 3.0 21.1 1.0
C58 A:6NC802 3.3 24.5 1.0
H631 A:6NC802 3.4 27.0 1.0
CG1 A:VAL471 3.5 27.6 1.0
C63 A:6NC802 3.5 22.5 1.0
O59 A:6NC802 3.6 26.9 1.0
C A:ALA481 3.6 25.1 1.0
C54 A:6NC802 3.7 23.1 1.0
C50 A:6NC802 3.7 27.9 1.0
N A:VAL482 3.7 25.6 1.0
CG2 A:VAL471 3.9 29.5 1.0
CA A:ALA481 3.9 22.5 1.0
C A:VAL482 4.0 28.5 1.0
O A:ALA481 4.0 26.0 1.0
N A:LYS483 4.1 26.4 1.0
C49 A:6NC802 4.1 28.3 1.0
CB A:VAL471 4.2 31.5 1.0
OG1 A:THR529 4.3 29.1 1.0
C60 A:6NC802 4.3 25.4 1.0
O A:VAL482 4.3 29.0 1.0
CA A:VAL482 4.3 24.7 1.0
CB A:LYS483 4.3 27.3 1.0
H501 A:6NC802 4.4 33.5 1.0
N62 A:6NC802 4.5 25.4 1.0
CA A:LYS483 4.6 24.9 1.0
F55 A:6NC802 4.8 20.9 1.0
CA A:VAL471 4.8 32.9 1.0
O A:ILE527 4.9 24.9 1.0
C61 A:6NC802 4.9 25.8 1.0

Fluorine binding site 5 out of 8 in 5jt2

Go back to Fluorine Binding Sites List in 5jt2
Fluorine binding site 5 out of 8 in the BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-Bisamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-Bisamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F801

b:28.2
occ:1.00
 F14 C:6NC801 0.0 28.2 1.0
C13 C:6NC801 1.3 28.4 1.0
C08 C:6NC801 2.4 27.5 1.0
H051 C:6NC801 2.4 32.5 1.0
C12 C:6NC801 2.4 26.1 1.0
N05 C:6NC801 2.7 27.1 1.0
C16 C:6NC801 2.9 25.9 1.0
O18 C:6NC801 3.1 28.5 1.0
OD2 D:ASP594 3.2 37.4 1.0
N D:ASP594 3.2 28.8 1.0
CE1 D:PHE583 3.3 28.8 1.0
CA D:GLY593 3.5 23.9 1.0
CD1 D:LEU514 3.6 22.0 1.0
C09 C:6NC801 3.6 26.6 1.0
C11 C:6NC801 3.6 26.5 1.0
C D:GLY593 3.7 28.9 1.0
CZ D:PHE583 3.8 26.3 1.0
C17 C:6NC801 3.9 27.3 1.0
CG D:ASP594 4.1 40.9 1.0
H221 C:6NC801 4.1 33.1 1.0
C10 C:6NC801 4.1 26.4 1.0
CA D:ASP594 4.2 31.9 1.0
CD1 D:PHE583 4.3 29.4 1.0
C22 C:6NC801 4.3 27.6 1.0
S04 C:6NC801 4.3 26.4 1.0
H091 C:6NC801 4.4 31.9 1.0
CB D:ASP594 4.5 37.9 1.0
NZ D:LYS483 4.5 35.7 1.0
H032 C:6NC801 4.6 26.2 1.0
N D:GLY593 4.6 27.9 1.0
H031 C:6NC801 4.7 26.2 1.0
O D:GLY593 4.7 30.7 1.0
F15 C:6NC801 4.7 26.4 1.0
C03 C:6NC801 4.8 21.8 1.0
CB D:ASN581 4.9 38.5 1.0
CG D:LEU514 4.9 26.2 1.0

Fluorine binding site 6 out of 8 in 5jt2

Go back to Fluorine Binding Sites List in 5jt2
Fluorine binding site 6 out of 8 in the BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-Bisamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-Bisamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F801

b:26.4
occ:1.00
 F15 C:6NC801 0.0 26.4 1.0
C11 C:6NC801 1.3 26.5 1.0
C12 C:6NC801 2.4 26.1 1.0
C10 C:6NC801 2.4 26.4 1.0
H101 C:6NC801 2.6 31.6 1.0
C16 C:6NC801 2.8 25.9 1.0
C17 C:6NC801 3.1 27.3 1.0
H221 C:6NC801 3.2 33.1 1.0
CB D:ALA481 3.2 25.0 1.0
C22 C:6NC801 3.3 27.6 1.0
O18 C:6NC801 3.6 28.5 1.0
C13 C:6NC801 3.6 28.4 1.0
C09 C:6NC801 3.6 26.6 1.0
CG1 D:VAL471 3.7 28.6 1.0
C D:ALA481 3.8 31.5 1.0
N D:VAL482 3.9 30.8 1.0
N D:LYS483 4.0 28.9 1.0
CG2 D:VAL471 4.0 27.5 1.0
C D:VAL482 4.1 29.5 1.0
CB D:LYS483 4.1 30.0 1.0
CA D:ALA481 4.1 26.0 1.0
C08 C:6NC801 4.1 27.5 1.0
OG1 D:THR529 4.1 28.3 1.0
O D:ALA481 4.2 30.2 1.0
C19 C:6NC801 4.2 26.2 1.0
N21 C:6NC801 4.3 31.2 1.0
CB D:VAL471 4.4 27.0 1.0
H091 C:6NC801 4.4 31.9 1.0
O D:VAL482 4.4 33.9 1.0
CA D:VAL482 4.4 26.0 1.0
CA D:LYS483 4.5 26.5 1.0
F14 C:6NC801 4.7 28.2 1.0
C20 C:6NC801 4.7 30.2 1.0
O D:ILE527 4.8 30.4 1.0
CG2 D:THR529 4.9 25.4 1.0

Fluorine binding site 7 out of 8 in 5jt2

Go back to Fluorine Binding Sites List in 5jt2
Fluorine binding site 7 out of 8 in the BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-Bisamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-Bisamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F801

b:30.7
occ:1.00
 F55 C:6NC801 0.0 30.7 1.0
C54 C:6NC801 1.4 34.6 1.0
H461 C:6NC801 2.3 43.2 1.0
C49 C:6NC801 2.4 36.7 1.0
C53 C:6NC801 2.4 34.8 1.0
N46 C:6NC801 2.6 36.0 1.0
C57 C:6NC801 2.8 38.2 1.0
CD1 C:LEU514 3.0 27.5 1.0
CE1 C:PHE583 3.2 29.1 1.0
O59 C:6NC801 3.2 39.2 1.0
CA C:GLY593 3.3 32.8 1.0
N C:ASP594 3.5 31.9 1.0
C50 C:6NC801 3.6 37.9 1.0
C52 C:6NC801 3.6 31.8 1.0
O C:HOH902 3.7 37.8 1.0
C C:GLY593 3.7 33.3 1.0
CZ C:PHE583 3.8 27.0 1.0
C58 C:6NC801 3.8 30.1 1.0
H631 C:6NC801 3.9 37.3 1.0
OD2 C:ASP594 4.0 49.2 1.0
CD1 C:PHE583 4.1 26.9 1.0
C51 C:6NC801 4.1 33.4 1.0
C63 C:6NC801 4.2 31.1 1.0
S45 C:6NC801 4.3 34.0 1.0
CG C:LEU514 4.4 32.5 1.0
H501 C:6NC801 4.4 45.5 1.0
N C:GLY593 4.4 29.5 1.0
CA C:ASP594 4.6 38.1 1.0
NZ C:LYS483 4.8 45.3 1.0
F56 C:6NC801 4.8 30.2 1.0
O C:GLY593 4.8 35.8 1.0
CG C:ASP594 4.9 48.8 1.0
C60 C:6NC801 4.9 32.4 1.0
H432 C:6NC801 5.0 38.0 1.0
O47 C:6NC801 5.0 31.0 1.0
CE2 C:PHE583 5.0 32.7 1.0
H442 C:6NC801 5.0 42.9 1.0

Fluorine binding site 8 out of 8 in 5jt2

Go back to Fluorine Binding Sites List in 5jt2
Fluorine binding site 8 out of 8 in the BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-Bisamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-Bisamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F801

b:30.2
occ:1.00
 F56 C:6NC801 0.0 30.2 1.0
C52 C:6NC801 1.4 31.8 1.0
C53 C:6NC801 2.4 34.8 1.0
C51 C:6NC801 2.4 33.4 1.0
H511 C:6NC801 2.6 40.1 1.0
C57 C:6NC801 2.9 38.2 1.0
CB C:ALA481 3.2 24.7 1.0
CG2 C:VAL471 3.4 44.8 1.0
CG1 C:VAL471 3.4 31.2 1.0
C58 C:6NC801 3.4 30.1 1.0
O59 C:6NC801 3.5 39.2 1.0
C54 C:6NC801 3.7 34.6 1.0
H631 C:6NC801 3.7 37.3 1.0
C50 C:6NC801 3.7 37.9 1.0
C63 C:6NC801 3.8 31.1 1.0
C C:ALA481 3.9 32.6 1.0
CB C:VAL471 3.9 38.4 1.0
N C:VAL482 4.0 29.6 1.0
N C:LYS483 4.0 30.3 1.0
CB C:LYS483 4.1 39.3 1.0
C C:VAL482 4.1 34.4 1.0
CA C:ALA481 4.1 24.4 1.0
O C:ALA481 4.1 26.8 1.0
C49 C:6NC801 4.1 36.7 1.0
CA C:LYS483 4.4 35.5 1.0
C60 C:6NC801 4.4 32.4 1.0
OG1 C:THR529 4.4 32.1 1.0
H501 C:6NC801 4.4 45.5 1.0
CA C:VAL482 4.5 31.7 1.0
O C:VAL482 4.5 35.6 1.0
CA C:VAL471 4.6 36.3 1.0
N62 C:6NC801 4.8 31.7 1.0
F55 C:6NC801 4.8 30.7 1.0
O C:ILE527 4.9 29.1 1.0

Reference:

M.Grasso, M.A.Estrada, C.Ventocilla, M.Samanta, J.Maksimoska, J.Villanueva, J.D.Winkler, R.Marmorstein. Chemically Linked Vemurafenib Inhibitors Promote An Inactive Braf(V600E) Conformation. Acs Chem.Biol. V. 11 2876 2016.
ISSN: ESSN 1554-8937
PubMed: 27571413
DOI: 10.1021/ACSCHEMBIO.6B00529
Page generated: Thu Aug 1 10:40:18 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