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Fluorine in PDB 4e4x: Crystal Structure of B-Raf Kinase Domain in Complex with A Dihydropyrido[2,3-D]Pyrimidinone-Based Inhibitor

Enzymatic activity of Crystal Structure of B-Raf Kinase Domain in Complex with A Dihydropyrido[2,3-D]Pyrimidinone-Based Inhibitor

All present enzymatic activity of Crystal Structure of B-Raf Kinase Domain in Complex with A Dihydropyrido[2,3-D]Pyrimidinone-Based Inhibitor:
2.7.11.1;

Protein crystallography data

The structure of Crystal Structure of B-Raf Kinase Domain in Complex with A Dihydropyrido[2,3-D]Pyrimidinone-Based Inhibitor, PDB code: 4e4x was solved by W.C.Voegtli, H.L.Sturgis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.86 / 3.60
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 109.000, 109.000, 155.210, 90.00, 90.00, 90.00
R / Rfree (%) 29.9 / 33.8

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of B-Raf Kinase Domain in Complex with A Dihydropyrido[2,3-D]Pyrimidinone-Based Inhibitor (pdb code 4e4x). 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 B-Raf Kinase Domain in Complex with A Dihydropyrido[2,3-D]Pyrimidinone-Based Inhibitor, PDB code: 4e4x:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 4e4x

Go back to Fluorine Binding Sites List in 4e4x
Fluorine binding site 1 out of 4 in the Crystal Structure of B-Raf Kinase Domain in Complex with A Dihydropyrido[2,3-D]Pyrimidinone-Based Inhibitor


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 B-Raf Kinase Domain in Complex with A Dihydropyrido[2,3-D]Pyrimidinone-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:53.7
occ:1.00
 F19 A:T1Q801 0.0 53.7 1.0
C18 A:T1Q801 1.4 50.6 1.0
C13 A:T1Q801 2.4 51.0 1.0
C17 A:T1Q801 2.4 49.4 1.0
C9 A:T1Q801 2.8 51.4 1.0
C10 A:T1Q801 3.3 51.1 1.0
CB A:ALA481 3.4 45.3 1.0
OG1 A:THR529 3.6 36.7 1.0
C14 A:T1Q801 3.7 50.5 1.0
C16 A:T1Q801 3.7 48.8 1.0
C8 A:T1Q801 3.7 52.0 1.0
C A:ALA481 3.7 46.4 1.0
N A:LYS483 3.7 56.6 1.0
O A:ALA481 3.7 44.7 1.0
CB A:LYS483 3.8 62.1 1.0
N A:VAL482 3.9 49.0 1.0
C A:VAL482 4.0 53.5 1.0
CG1 A:VAL471 4.0 56.0 1.0
O12 A:T1Q801 4.0 51.9 1.0
C15 A:T1Q801 4.2 49.5 1.0
CA A:ALA481 4.2 45.3 1.0
CA A:VAL482 4.3 51.6 1.0
CA A:LYS483 4.3 61.1 1.0
CG2 A:THR529 4.3 38.5 1.0
C5 A:T1Q801 4.4 52.2 1.0
O A:VAL482 4.5 53.2 1.0
O A:ILE527 4.5 45.1 1.0
CB A:THR529 4.5 37.6 1.0
N7 A:T1Q801 4.6 52.4 1.0
N A:THR529 4.6 38.6 1.0
F20 A:T1Q801 4.8 53.3 1.0
CD A:LYS483 4.8 65.3 1.0
CG2 A:VAL471 4.9 57.3 1.0
CG A:LYS483 4.9 64.3 1.0
C4 A:T1Q801 5.0 52.9 1.0

Fluorine binding site 2 out of 4 in 4e4x

Go back to Fluorine Binding Sites List in 4e4x
Fluorine binding site 2 out of 4 in the Crystal Structure of B-Raf Kinase Domain in Complex with A Dihydropyrido[2,3-D]Pyrimidinone-Based Inhibitor


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 B-Raf Kinase Domain in Complex with A Dihydropyrido[2,3-D]Pyrimidinone-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:53.3
occ:1.00
 F20 A:T1Q801 0.0 53.3 1.0
C14 A:T1Q801 1.4 50.5 1.0
C13 A:T1Q801 2.4 51.0 1.0
C15 A:T1Q801 2.4 49.5 1.0
N21 A:T1Q801 2.8 49.8 1.0
C9 A:T1Q801 2.8 51.4 1.0
C8 A:T1Q801 3.3 52.0 1.0
O12 A:T1Q801 3.3 51.9 1.0
CD2 A:LEU514 3.3 35.1 1.0
N A:ASP594 3.4 45.7 1.0
C10 A:T1Q801 3.7 51.1 1.0
C18 A:T1Q801 3.7 50.6 1.0
C16 A:T1Q801 3.7 48.8 1.0
CA A:GLY593 3.9 41.5 1.0
CE1 A:PHE583 3.9 34.4 1.0
C A:GLY593 4.0 44.8 1.0
CA A:ASP594 4.1 46.8 1.0
C17 A:T1Q801 4.2 49.4 1.0
CZ A:PHE583 4.2 34.0 1.0
CB A:ASP594 4.3 47.5 1.0
N7 A:T1Q801 4.3 52.4 1.0
S23 A:T1Q801 4.4 50.2 1.0
C5 A:T1Q801 4.7 52.2 1.0
F19 A:T1Q801 4.8 53.7 1.0
CG A:LEU514 4.8 34.7 1.0
O A:GLY593 4.9 47.3 1.0
C4 A:T1Q801 5.0 52.9 1.0

Fluorine binding site 3 out of 4 in 4e4x

Go back to Fluorine Binding Sites List in 4e4x
Fluorine binding site 3 out of 4 in the Crystal Structure of B-Raf Kinase Domain in Complex with A Dihydropyrido[2,3-D]Pyrimidinone-Based Inhibitor


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 B-Raf Kinase Domain in Complex with A Dihydropyrido[2,3-D]Pyrimidinone-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:48.9
occ:1.00
 F19 B:T1Q801 0.0 48.9 1.0
C18 B:T1Q801 1.4 46.5 1.0
C13 B:T1Q801 2.4 46.4 1.0
C17 B:T1Q801 2.4 46.0 1.0
C9 B:T1Q801 2.8 45.8 1.0
CB B:ALA481 3.3 45.0 1.0
C10 B:T1Q801 3.4 46.5 1.0
C8 B:T1Q801 3.5 45.2 1.0
C B:ALA481 3.7 45.9 1.0
C14 B:T1Q801 3.7 45.8 1.0
C16 B:T1Q801 3.7 45.6 1.0
CG1 B:VAL471 3.7 54.1 1.0
OG1 B:THR529 3.7 36.9 1.0
N B:LYS483 3.7 56.8 1.0
O B:ALA481 3.8 45.7 1.0
CB B:LYS483 3.8 61.5 1.0
O12 B:T1Q801 3.8 43.2 1.0
N B:VAL482 3.9 47.1 1.0
C B:VAL482 3.9 53.2 1.0
CA B:ALA481 4.1 45.0 1.0
C15 B:T1Q801 4.2 44.9 1.0
CA B:VAL482 4.2 50.2 1.0
CA B:LYS483 4.2 60.5 1.0
O B:VAL482 4.3 53.8 1.0
C5 B:T1Q801 4.5 46.2 1.0
N7 B:T1Q801 4.5 46.5 1.0
CG2 B:THR529 4.6 38.1 1.0
O B:ILE527 4.6 43.6 1.0
CG2 B:VAL471 4.7 54.8 1.0
CB B:THR529 4.7 37.1 1.0
CB B:VAL471 4.8 54.7 1.0
F20 B:T1Q801 4.8 47.8 1.0
CD B:LYS483 4.8 66.1 1.0
N B:THR529 4.8 36.5 1.0
CG B:LYS483 4.9 64.5 1.0
C4 B:T1Q801 5.0 46.5 1.0

Fluorine binding site 4 out of 4 in 4e4x

Go back to Fluorine Binding Sites List in 4e4x
Fluorine binding site 4 out of 4 in the Crystal Structure of B-Raf Kinase Domain in Complex with A Dihydropyrido[2,3-D]Pyrimidinone-Based Inhibitor


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 B-Raf Kinase Domain in Complex with A Dihydropyrido[2,3-D]Pyrimidinone-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:47.8
occ:1.00
 F20 B:T1Q801 0.0 47.8 1.0
C14 B:T1Q801 1.4 45.8 1.0
C13 B:T1Q801 2.4 46.4 1.0
C15 B:T1Q801 2.4 44.9 1.0
N21 B:T1Q801 2.8 42.8 1.0
C9 B:T1Q801 2.8 45.8 1.0
CD2 B:LEU514 3.1 34.5 1.0
C8 B:T1Q801 3.4 45.2 1.0
O12 B:T1Q801 3.5 43.2 1.0
C10 B:T1Q801 3.5 46.5 1.0
CE1 B:PHE583 3.7 31.5 1.0
C18 B:T1Q801 3.7 46.5 1.0
C16 B:T1Q801 3.7 45.6 1.0
N B:ASP594 3.7 44.0 1.0
CA B:GLY593 4.0 39.5 1.0
CZ B:PHE583 4.0 30.3 1.0
C B:GLY593 4.1 41.9 1.0
C17 B:T1Q801 4.2 46.0 1.0
CA B:ASP594 4.4 46.6 1.0
N7 B:T1Q801 4.4 46.5 1.0
S23 B:T1Q801 4.4 40.4 1.0
C27 B:T1Q801 4.5 34.1 1.0
CB B:ASP594 4.5 47.1 1.0
CG B:LEU514 4.6 35.8 1.0
C5 B:T1Q801 4.6 46.2 1.0
F19 B:T1Q801 4.8 48.9 1.0
CD1 B:PHE583 4.9 32.8 1.0
C4 B:T1Q801 4.9 46.5 1.0

Reference:

L.Ren, K.A.Ahrendt, J.Grina, E.R.Laird, A.J.Buckmelter, J.D.Hansen, B.Newhouse, D.Moreno, S.Wenglowsky, V.Dinkel, S.L.Gloor, G.Hastings, S.Rana, K.Rasor, T.Risom, H.L.Sturgis, W.C.Voegtli, S.Mathieu. The Discovery of Potent and Selective Pyridopyrimidin-7-One Based Inhibitors of B-Raf(V600E) Kinase. Bioorg.Med.Chem.Lett. V. 22 3387 2012.
ISSN: ISSN 0960-894X
PubMed: 22534450
DOI: 10.1016/J.BMCL.2012.04.015
Page generated: Thu Aug 1 01:16:34 2024

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