Fluorine in PDB 8f7p: Braf Kinase in Complex with LXH254 (Naporafenib)

Enzymatic activity of Braf Kinase in Complex with LXH254 (Naporafenib)

All present enzymatic activity of Braf Kinase in Complex with LXH254 (Naporafenib):
2.7.11.1;

Protein crystallography data

The structure of Braf Kinase in Complex with LXH254 (Naporafenib), PDB code: 8f7p was solved by E.Tkacik, K.Li, G.Gonzalez Del-Pino, M.J.Eck, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.75 / 2.74
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.647, 101.746, 58.688, 90, 109.67, 90
R / Rfree (%) 21.4 / 25.8

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Braf Kinase in Complex with LXH254 (Naporafenib) (pdb code 8f7p). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Braf Kinase in Complex with LXH254 (Naporafenib), PDB code: 8f7p:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 8f7p

Go back to Fluorine Binding Sites List in 8f7p
Fluorine binding site 1 out of 6 in the Braf Kinase in Complex with LXH254 (Naporafenib)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Braf Kinase in Complex with LXH254 (Naporafenib) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:53.2
occ:1.00
 F30 A:K81801 0.0 53.2 1.0
C29 A:K81801 1.3 51.1 1.0
F36 A:K81801 2.2 49.7 1.0
F33 A:K81801 2.2 46.5 1.0
C27 A:K81801 2.4 52.7 1.0
N26 A:K81801 3.1 53.9 1.0
C28 A:K81801 3.2 59.1 1.0
CG2 A:ILE513 3.4 31.6 1.0
CD2 A:LEU567 3.6 42.1 1.0
CG2 A:THR508 3.9 35.9 1.0
CD2 A:LEU505 4.0 41.2 1.0
C25 A:K81801 4.4 52.8 1.0
CD1 A:LEU567 4.5 42.0 1.0
C22 A:K81801 4.5 59.2 1.0
CG A:LEU567 4.6 43.4 1.0
CB A:THR508 4.7 44.5 1.0
OG1 A:THR508 4.7 42.5 1.0
CB A:ILE513 4.8 33.7 1.0
O A:ILE592 4.9 39.5 1.0
C24 A:K81801 5.0 58.0 1.0
CD1 A:ILE513 5.0 39.6 1.0

Fluorine binding site 2 out of 6 in 8f7p

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Fluorine binding site 2 out of 6 in the Braf Kinase in Complex with LXH254 (Naporafenib)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Braf Kinase in Complex with LXH254 (Naporafenib) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:46.5
occ:1.00
 F33 A:K81801 0.0 46.5 1.0
C29 A:K81801 1.4 51.1 1.0
F30 A:K81801 2.2 53.2 1.0
F36 A:K81801 2.2 49.7 1.0
C27 A:K81801 2.4 52.7 1.0
N26 A:K81801 2.8 53.9 1.0
C28 A:K81801 3.6 59.1 1.0
CD1 A:LEU567 3.8 42.0 1.0
CD2 A:LEU567 3.9 42.1 1.0
CD2 A:HIS574 4.0 48.0 1.0
C25 A:K81801 4.2 52.8 1.0
CG2 A:ILE572 4.4 40.8 1.0
CG A:LEU567 4.5 43.4 1.0
NE2 A:HIS574 4.6 52.3 1.0
CG A:HIS574 4.7 46.3 1.0
C22 A:K81801 4.8 59.2 1.0

Fluorine binding site 3 out of 6 in 8f7p

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Fluorine binding site 3 out of 6 in the Braf Kinase in Complex with LXH254 (Naporafenib)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Braf Kinase in Complex with LXH254 (Naporafenib) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:49.7
occ:1.00
 F36 A:K81801 0.0 49.7 1.0
C29 A:K81801 1.3 51.1 1.0
F30 A:K81801 2.2 53.2 1.0
F33 A:K81801 2.2 46.5 1.0
C27 A:K81801 2.4 52.7 1.0
C28 A:K81801 2.7 59.1 1.0
CA A:GLY593 3.4 48.2 1.0
O A:ILE592 3.4 39.5 1.0
N26 A:K81801 3.6 53.9 1.0
CG2 A:ILE513 3.9 31.6 1.0
C A:ILE592 3.9 45.8 1.0
N A:GLY593 3.9 46.6 1.0
C A:GLY593 4.0 50.4 1.0
C22 A:K81801 4.1 59.2 1.0
CD2 A:HIS574 4.3 48.0 1.0
N A:ASP594 4.4 51.8 1.0
CD1 A:LEU567 4.4 42.0 1.0
NE2 A:HIS574 4.5 52.3 1.0
CG2 A:ILE592 4.5 39.3 1.0
O A:GLY593 4.5 54.3 1.0
C25 A:K81801 4.7 52.8 1.0
CD2 A:LEU567 4.7 42.1 1.0
O23 A:K81801 4.9 56.0 1.0
CD1 A:ILE513 4.9 39.6 1.0
C24 A:K81801 5.0 58.0 1.0

Fluorine binding site 4 out of 6 in 8f7p

Go back to Fluorine Binding Sites List in 8f7p
Fluorine binding site 4 out of 6 in the Braf Kinase in Complex with LXH254 (Naporafenib)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Braf Kinase in Complex with LXH254 (Naporafenib) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:53.2
occ:1.00
 F30 B:K81801 0.0 53.2 1.0
C29 B:K81801 1.3 52.5 1.0
F36 B:K81801 2.2 43.8 1.0
F33 B:K81801 2.2 57.6 1.0
C27 B:K81801 2.4 49.8 1.0
C28 B:K81801 2.7 51.9 1.0
N26 B:K81801 3.6 51.8 1.0
CA B:GLY593 3.8 45.2 1.0
O B:ILE592 4.0 41.3 1.0
CD2 B:HIS574 4.0 41.8 1.0
C22 B:K81801 4.1 52.9 1.0
C B:GLY593 4.2 44.8 1.0
NE2 B:HIS574 4.2 47.2 1.0
CG2 B:ILE513 4.3 34.3 1.0
CD1 B:LEU567 4.4 39.9 1.0
N B:GLY593 4.4 41.8 1.0
C B:ILE592 4.4 41.4 1.0
N B:ASP594 4.5 49.3 1.0
CD2 B:LEU567 4.6 39.9 1.0
C25 B:K81801 4.7 53.8 1.0
O B:GLY593 4.7 47.0 1.0
CD2 B:LEU505 4.9 44.5 1.0
CG2 B:ILE592 4.9 34.3 1.0
C24 B:K81801 5.0 56.3 1.0
O23 B:K81801 5.0 54.8 1.0

Fluorine binding site 5 out of 6 in 8f7p

Go back to Fluorine Binding Sites List in 8f7p
Fluorine binding site 5 out of 6 in the Braf Kinase in Complex with LXH254 (Naporafenib)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Braf Kinase in Complex with LXH254 (Naporafenib) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:57.6
occ:1.00
 F33 B:K81801 0.0 57.6 1.0
C29 B:K81801 1.4 52.5 1.0
F30 B:K81801 2.2 53.2 1.0
F36 B:K81801 2.2 43.8 1.0
C27 B:K81801 2.4 49.8 1.0
N26 B:K81801 3.2 51.8 1.0
C28 B:K81801 3.3 51.9 1.0
CD2 B:LEU567 4.0 39.9 1.0
CD2 B:LEU505 4.1 44.5 1.0
CG2 B:VAL504 4.2 46.6 1.0
CG2 B:THR508 4.3 42.3 1.0
C25 B:K81801 4.4 53.8 1.0
O B:VAL504 4.5 54.4 1.0
C22 B:K81801 4.5 52.9 1.0
CG2 B:ILE572 4.6 42.6 1.0
CG2 B:ILE513 4.7 34.3 1.0
CD1 B:LEU567 4.8 39.9 1.0
C B:VAL504 4.9 48.1 1.0
CB B:VAL504 4.9 48.3 1.0
C24 B:K81801 5.0 56.3 1.0

Fluorine binding site 6 out of 6 in 8f7p

Go back to Fluorine Binding Sites List in 8f7p
Fluorine binding site 6 out of 6 in the Braf Kinase in Complex with LXH254 (Naporafenib)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Braf Kinase in Complex with LXH254 (Naporafenib) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:43.8
occ:1.00
 F36 B:K81801 0.0 43.8 1.0
C29 B:K81801 1.3 52.5 1.0
F30 B:K81801 2.2 53.2 1.0
F33 B:K81801 2.2 57.6 1.0
C27 B:K81801 2.4 49.8 1.0
N26 B:K81801 2.8 51.8 1.0
CD2 B:HIS574 3.4 41.8 1.0
C28 B:K81801 3.6 51.9 1.0
CG B:HIS574 4.0 44.0 1.0
NE2 B:HIS574 4.0 47.2 1.0
CD1 B:LEU567 4.1 39.9 1.0
C25 B:K81801 4.1 53.8 1.0
CA B:HIS574 4.3 40.9 1.0
CD2 B:LEU567 4.4 39.9 1.0
CB B:HIS574 4.5 36.9 1.0
CG2 B:ILE572 4.5 42.6 1.0
C22 B:K81801 4.7 52.9 1.0
CE1 B:HIS574 4.7 47.3 1.0
ND1 B:HIS574 4.7 40.8 1.0
O B:HIS574 4.9 35.9 1.0
CG B:LEU567 4.9 43.7 1.0
C24 B:K81801 5.0 56.3 1.0

Reference:

E.Tkacik, K.Li, G.Gonzalez-Del Pino, B.H.Ha, J.Vinals, E.Park, T.S.Beyett, M.J.Eck. Structure and Raf-Family Kinase Isoform Selectivity of Type II Raf Inhibitors Tovorafenib and Naporafenib. J.Biol.Chem. 04634 2023.
ISSN: ESSN 1083-351X
PubMed: 36963492
DOI: 10.1016/J.JBC.2023.104634
Page generated: Tue Apr 25 20:18:21 2023

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