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Fluorine in PDB 6cad: Crystal Structure of Raf Kinase Domain Bound to the Inhibitor 2A

Enzymatic activity of Crystal Structure of Raf Kinase Domain Bound to the Inhibitor 2A

All present enzymatic activity of Crystal Structure of Raf Kinase Domain Bound to the Inhibitor 2A:
2.7.11.1;

Protein crystallography data

The structure of Crystal Structure of Raf Kinase Domain Bound to the Inhibitor 2A, PDB code: 6cad was solved by P.Maisonneuve, I.Kurinov, A.Assadieskandar, C.Yu, X.Liu, Y.-C.Chen, G.K.S.Prakash, C.Zhang, F.Sicheri, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.58 / 2.55
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 85.493, 114.548, 55.599, 90.00, 90.00, 90.00
R / Rfree (%) 25.5 / 27.7

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Raf Kinase Domain Bound to the Inhibitor 2A (pdb code 6cad). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Raf Kinase Domain Bound to the Inhibitor 2A, PDB code: 6cad:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 6cad

Go back to Fluorine Binding Sites List in 6cad
Fluorine binding site 1 out of 6 in the Crystal Structure of Raf Kinase Domain Bound to the Inhibitor 2A


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 Raf Kinase Domain Bound to the Inhibitor 2A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:81.5
occ:1.00
 F26 A:EU4801 0.0 81.5 1.0
C25 A:EU4801 1.4 86.2 1.0
F27 A:EU4801 2.2 77.9 1.0
F28 A:EU4801 2.2 86.6 1.0
C21 A:EU4801 2.4 83.5 1.0
ND1 A:HIS574 2.9 0.4 1.0
C20 A:EU4801 3.0 70.5 1.0
CE1 A:HIS574 3.0 0.0 1.0
CA A:GLY593 3.2 99.0 1.0
C A:GLY593 3.3 91.3 1.0
C22 A:EU4801 3.4 96.5 1.0
N A:GLY593 3.6 98.0 1.0
N A:ASP594 3.6 0.0 1.0
O A:GLY593 3.8 80.8 1.0
O A:ILE592 3.9 85.9 1.0
C A:ILE592 4.0 80.3 1.0
CG A:HIS574 4.0 0.4 1.0
CG2 A:ILE592 4.1 93.2 1.0
NE2 A:HIS574 4.1 0.0 1.0
C19 A:EU4801 4.3 78.5 1.0
CA A:ASP594 4.5 0.4 1.0
C23 A:EU4801 4.6 96.1 1.0
CD2 A:HIS574 4.6 0.4 1.0
CB A:ASP594 4.6 0.1 1.0
CD1 A:LEU567 4.8 68.9 1.0
CB A:HIS574 4.8 1.0 1.0
C24 A:EU4801 4.9 86.1 1.0
CB A:ILE592 5.0 81.8 1.0

Fluorine binding site 2 out of 6 in 6cad

Go back to Fluorine Binding Sites List in 6cad
Fluorine binding site 2 out of 6 in the Crystal Structure of Raf Kinase Domain Bound to the Inhibitor 2A


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 Raf Kinase Domain Bound to the Inhibitor 2A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:77.9
occ:1.00
 F27 A:EU4801 0.0 77.9 1.0
C25 A:EU4801 1.4 86.2 1.0
F28 A:EU4801 2.2 86.6 1.0
F26 A:EU4801 2.2 81.5 1.0
C21 A:EU4801 2.4 83.5 1.0
C20 A:EU4801 2.9 70.5 1.0
C22 A:EU4801 3.5 96.5 1.0
O A:ILE592 3.6 85.9 1.0
CG2 A:ILE513 3.9 63.5 1.0
CA A:GLY593 4.0 99.0 1.0
C19 A:EU4801 4.2 78.5 1.0
CD2 A:LEU505 4.3 69.0 1.0
C A:ILE592 4.3 80.3 1.0
N A:GLY593 4.5 98.0 1.0
C23 A:EU4801 4.6 96.1 1.0
CD1 A:LEU567 4.6 68.9 1.0
C A:GLY593 4.8 91.3 1.0
CD2 A:LEU567 4.8 66.5 1.0
ND1 A:HIS574 4.9 0.4 1.0
C24 A:EU4801 4.9 86.1 1.0
N A:ASP594 5.0 0.0 1.0

Fluorine binding site 3 out of 6 in 6cad

Go back to Fluorine Binding Sites List in 6cad
Fluorine binding site 3 out of 6 in the Crystal Structure of Raf Kinase Domain Bound to the Inhibitor 2A


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 Raf Kinase Domain Bound to the Inhibitor 2A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:86.6
occ:1.00
 F28 A:EU4801 0.0 86.6 1.0
C25 A:EU4801 1.4 86.2 1.0
F27 A:EU4801 2.2 77.9 1.0
F26 A:EU4801 2.2 81.5 1.0
C21 A:EU4801 2.4 83.5 1.0
C22 A:EU4801 2.7 96.5 1.0
ND1 A:HIS574 3.4 0.4 1.0
C20 A:EU4801 3.7 70.5 1.0
CD1 A:LEU567 3.9 68.9 1.0
C23 A:EU4801 4.1 96.1 1.0
CE1 A:HIS574 4.2 0.0 1.0
CG A:HIS574 4.3 0.4 1.0
CB A:HIS574 4.4 1.0 1.0
CD2 A:LEU567 4.6 66.5 1.0
C19 A:EU4801 4.8 78.5 1.0
CG A:LEU567 4.9 73.0 1.0
C24 A:EU4801 4.9 86.1 1.0
CA A:HIS574 4.9 0.6 1.0
CG2 A:ILE572 4.9 77.9 1.0

Fluorine binding site 4 out of 6 in 6cad

Go back to Fluorine Binding Sites List in 6cad
Fluorine binding site 4 out of 6 in the Crystal Structure of Raf Kinase Domain Bound to the Inhibitor 2A


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 Raf Kinase Domain Bound to the Inhibitor 2A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:80.9
occ:1.00
 F26 B:EU4801 0.0 80.9 1.0
C25 B:EU4801 1.4 89.3 1.0
F27 B:EU4801 2.2 97.2 1.0
F28 B:EU4801 2.2 0.4 1.0
C21 B:EU4801 2.4 75.6 1.0
C22 B:EU4801 2.8 70.5 1.0
C20 B:EU4801 3.5 68.2 1.0
CD1 B:LEU567 4.2 88.0 1.0
C23 B:EU4801 4.2 59.5 1.0
CD2 B:LEU567 4.4 82.5 1.0
CG2 B:ILE513 4.7 61.2 1.0
C19 B:EU4801 4.7 63.5 1.0
CD2 B:LEU505 4.8 87.1 1.0
CG2 B:THR508 4.9 88.4 1.0
C24 B:EU4801 4.9 55.5 1.0
O B:ILE592 4.9 78.3 1.0
CG B:LEU567 5.0 86.1 1.0

Fluorine binding site 5 out of 6 in 6cad

Go back to Fluorine Binding Sites List in 6cad
Fluorine binding site 5 out of 6 in the Crystal Structure of Raf Kinase Domain Bound to the Inhibitor 2A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Raf Kinase Domain Bound to the Inhibitor 2A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:97.2
occ:1.00
 F27 B:EU4801 0.0 97.2 1.0
C25 B:EU4801 1.4 89.3 1.0
F28 B:EU4801 2.2 0.4 1.0
F26 B:EU4801 2.2 80.9 1.0
C21 B:EU4801 2.4 75.6 1.0
C22 B:EU4801 3.1 70.5 1.0
C20 B:EU4801 3.3 68.2 1.0
ND1 B:HIS574 3.6 74.9 1.0
CE1 B:HIS574 3.6 75.9 1.0
CG B:HIS574 3.7 75.2 1.0
CA B:GLY593 3.7 84.4 1.0
NE2 B:HIS574 3.8 75.5 1.0
CD2 B:HIS574 3.8 79.2 1.0
C B:GLY593 3.9 85.8 1.0
N B:GLY593 4.1 84.4 1.0
N B:ASP594 4.2 84.2 1.0
CG2 B:ILE592 4.2 75.1 1.0
O B:GLY593 4.2 78.8 1.0
O B:ILE592 4.3 78.3 1.0
C23 B:EU4801 4.3 59.5 1.0
C B:ILE592 4.4 85.9 1.0
CB B:HIS574 4.4 80.7 1.0
CD1 B:LEU567 4.5 88.0 1.0
C19 B:EU4801 4.5 63.5 1.0
C24 B:EU4801 4.9 55.5 1.0

Fluorine binding site 6 out of 6 in 6cad

Go back to Fluorine Binding Sites List in 6cad
Fluorine binding site 6 out of 6 in the Crystal Structure of Raf Kinase Domain Bound to the Inhibitor 2A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Raf Kinase Domain Bound to the Inhibitor 2A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:0.4
occ:1.00
 F28 B:EU4801 0.0 0.4 1.0
C25 B:EU4801 1.4 89.3 1.0
F27 B:EU4801 2.2 97.2 1.0
F26 B:EU4801 2.2 80.9 1.0
C21 B:EU4801 2.4 75.6 1.0
C20 B:EU4801 2.7 68.2 1.0
O B:ILE592 2.9 78.3 1.0
CA B:GLY593 3.3 84.4 1.0
C B:ILE592 3.6 85.9 1.0
C22 B:EU4801 3.6 70.5 1.0
N B:GLY593 3.8 84.4 1.0
CG2 B:ILE513 4.0 61.2 1.0
C19 B:EU4801 4.1 63.5 1.0
C B:GLY593 4.1 85.8 1.0
N B:ASP594 4.4 84.2 1.0
CG2 B:ILE592 4.6 75.1 1.0
N B:LEU514 4.7 88.8 1.0
CD2 B:LEU505 4.7 87.1 1.0
C23 B:EU4801 4.8 59.5 1.0
CA B:ILE592 4.8 74.7 1.0
CB B:LEU514 4.9 70.2 1.0
CB B:ILE592 4.9 75.6 1.0
C24 B:EU4801 4.9 55.5 1.0
O B:GLY593 4.9 78.8 1.0
C13 B:EU4801 5.0 65.8 1.0

Reference:

A.Assadieskandar, C.Yu, P.Maisonneuve, X.Liu, Y.C.Chen, G.K.S.Prakash, I.Kurinov, F.Sicheri, C.Zhang. Effects of Rigidity on the Selectivity of Protein Kinase Inhibitors. Eur J Med Chem V. 146 519 2018.
ISSN: ISSN 1768-3254
PubMed: 29407977
DOI: 10.1016/J.EJMECH.2018.01.053
Page generated: Thu Aug 1 18:29:47 2024

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