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Fluorine in PDB 3cpc: Crystal Structure of the VEGFR2 Kinase Domain in Complex with A Pyridone Inhibitor

Enzymatic activity of Crystal Structure of the VEGFR2 Kinase Domain in Complex with A Pyridone Inhibitor

All present enzymatic activity of Crystal Structure of the VEGFR2 Kinase Domain in Complex with A Pyridone Inhibitor:
2.7.10.1;

Protein crystallography data

The structure of Crystal Structure of the VEGFR2 Kinase Domain in Complex with A Pyridone Inhibitor, PDB code: 3cpc was solved by D.A.Whittington, A.M.Long, P.Rose, Y.Gu, H.Zhao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.361, 66.865, 89.858, 90.00, 93.35, 90.00
R / Rfree (%) 21.8 / 27.2

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the VEGFR2 Kinase Domain in Complex with A Pyridone Inhibitor (pdb code 3cpc). 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 the VEGFR2 Kinase Domain in Complex with A Pyridone Inhibitor, PDB code: 3cpc:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3cpc

Go back to Fluorine Binding Sites List in 3cpc
Fluorine binding site 1 out of 6 in the Crystal Structure of the VEGFR2 Kinase Domain in Complex with A Pyridone 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 the VEGFR2 Kinase Domain in Complex with A Pyridone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1

b:28.2
occ:1.00
 F2 A:C521 0.0 28.2 1.0
C21 A:C521 1.3 27.0 1.0
F1 A:C521 2.1 26.9 1.0
F3 A:C521 2.2 26.9 1.0
C17 A:C521 2.4 26.8 1.0
C18 A:C521 3.0 26.5 1.0
CD2 A:LEU889 3.5 34.6 1.0
C16 A:C521 3.5 26.1 1.0
CG1 A:VAL898 3.7 27.0 1.0
C19 A:C521 4.3 26.3 1.0
CD2 A:LEU1019 4.5 27.1 1.0
CD1 A:ILE892 4.6 35.6 1.0
C15 A:C521 4.6 25.8 1.0
CG A:LEU889 4.7 34.3 1.0
CD1 A:LEU1019 4.8 27.3 1.0
O A:ILE1044 4.9 27.6 1.0
C20 A:C521 5.0 26.4 1.0

Fluorine binding site 2 out of 6 in 3cpc

Go back to Fluorine Binding Sites List in 3cpc
Fluorine binding site 2 out of 6 in the Crystal Structure of the VEGFR2 Kinase Domain in Complex with A Pyridone 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 the VEGFR2 Kinase Domain in Complex with A Pyridone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1

b:26.9
occ:1.00
 F3 A:C521 0.0 26.9 1.0
C21 A:C521 1.3 27.0 1.0
F2 A:C521 2.2 28.2 1.0
F1 A:C521 2.2 26.9 1.0
C17 A:C521 2.3 26.8 1.0
C18 A:C521 2.9 26.5 1.0
C16 A:C521 3.3 26.1 1.0
CD2 A:HIS1026 3.7 34.5 1.0
NE2 A:HIS1026 3.8 34.1 1.0
C A:CYS1045 3.9 31.5 1.0
CG2 A:ILE1044 3.9 27.1 1.0
O A:CYS1045 3.9 31.7 1.0
O A:ILE1044 4.1 27.6 1.0
CB A:ASP1046 4.2 34.7 1.0
CA A:CYS1045 4.2 30.3 1.0
C19 A:C521 4.2 26.3 1.0
N A:ASP1046 4.3 32.8 1.0
C A:ILE1044 4.4 28.0 1.0
N A:CYS1045 4.5 28.8 1.0
C15 A:C521 4.5 25.8 1.0
CD1 A:LEU1019 4.8 27.3 1.0
CG1 A:VAL898 4.8 27.0 1.0
CA A:ASP1046 4.8 34.4 1.0
CB A:ILE1044 4.8 27.1 1.0
C20 A:C521 4.9 26.4 1.0
CG A:HIS1026 4.9 34.6 1.0
OD2 A:ASP1046 5.0 37.4 1.0

Fluorine binding site 3 out of 6 in 3cpc

Go back to Fluorine Binding Sites List in 3cpc
Fluorine binding site 3 out of 6 in the Crystal Structure of the VEGFR2 Kinase Domain in Complex with A Pyridone 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 the VEGFR2 Kinase Domain in Complex with A Pyridone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1

b:26.9
occ:1.00
 F1 A:C521 0.0 26.9 1.0
C21 A:C521 1.3 27.0 1.0
F2 A:C521 2.1 28.2 1.0
F3 A:C521 2.2 26.9 1.0
C17 A:C521 2.4 26.8 1.0
C16 A:C521 2.7 26.1 1.0
O A:ILE1044 3.0 27.6 1.0
CG1 A:VAL898 3.4 27.0 1.0
CG1 A:VAL899 3.5 26.3 1.0
C18 A:C521 3.7 26.5 1.0
C A:ILE1044 3.8 28.0 1.0
CA A:CYS1045 3.9 30.3 1.0
N A:VAL899 4.1 27.0 1.0
C15 A:C521 4.1 25.8 1.0
N A:CYS1045 4.2 28.8 1.0
CD2 A:LEU889 4.3 34.6 1.0
C A:CYS1045 4.4 31.5 1.0
O A:VAL899 4.5 27.1 1.0
CB A:VAL899 4.5 26.8 1.0
CG2 A:ILE1044 4.6 27.1 1.0
O1 A:C521 4.6 25.1 1.0
CB A:VAL898 4.6 26.9 1.0
N A:ASP1046 4.8 32.8 1.0
CA A:VAL899 4.8 26.7 1.0
C A:VAL898 4.8 27.0 1.0
C19 A:C521 4.8 26.3 1.0
CA A:VAL898 4.8 26.9 1.0
CB A:ILE1044 4.8 27.1 1.0
O A:CYS1045 4.8 31.7 1.0
CA A:ILE1044 4.9 27.3 1.0
N4 A:C521 5.0 26.0 1.0
C20 A:C521 5.0 26.4 1.0

Fluorine binding site 4 out of 6 in 3cpc

Go back to Fluorine Binding Sites List in 3cpc
Fluorine binding site 4 out of 6 in the Crystal Structure of the VEGFR2 Kinase Domain in Complex with A Pyridone 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 the VEGFR2 Kinase Domain in Complex with A Pyridone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2

b:30.9
occ:1.00
 F2 B:C522 0.0 30.9 1.0
C21 B:C522 1.3 29.9 1.0
F1 B:C522 2.2 31.4 1.0
F3 B:C522 2.2 30.3 1.0
C17 B:C522 2.3 29.4 1.0
C18 B:C522 2.8 29.1 1.0
C16 B:C522 3.6 29.1 1.0
C19 B:C522 4.1 28.9 1.0
CG1 B:VAL898 4.2 37.2 1.0
CD1 B:ILE892 4.3 45.8 1.0
CD2 B:LEU889 4.4 45.5 1.0
CD2 B:LEU1019 4.5 38.9 1.0
CD1 B:LEU1019 4.7 38.9 1.0
C15 B:C522 4.7 28.3 1.0
C20 B:C522 4.9 28.9 1.0
CD2 B:HIS1026 4.9 39.9 1.0

Fluorine binding site 5 out of 6 in 3cpc

Go back to Fluorine Binding Sites List in 3cpc
Fluorine binding site 5 out of 6 in the Crystal Structure of the VEGFR2 Kinase Domain in Complex with A Pyridone Inhibitor


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 the VEGFR2 Kinase Domain in Complex with A Pyridone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2

b:30.3
occ:1.00
 F3 B:C522 0.0 30.3 1.0
C21 B:C522 1.3 29.9 1.0
F1 B:C522 2.2 31.4 1.0
F2 B:C522 2.2 30.9 1.0
C17 B:C522 2.3 29.4 1.0
C18 B:C522 3.1 29.1 1.0
C16 B:C522 3.2 29.1 1.0
C B:CYS1045 3.5 34.7 1.0
CG2 B:ILE1044 3.5 31.8 1.0
O B:CYS1045 3.6 34.5 1.0
NE2 B:HIS1026 3.6 39.2 1.0
CD2 B:HIS1026 3.6 39.9 1.0
CA B:CYS1045 3.7 34.3 1.0
O B:ILE1044 3.8 32.7 1.0
N B:ASP1046 3.9 35.8 1.0
N B:CYS1045 4.0 33.5 1.0
C B:ILE1044 4.0 33.1 1.0
CB B:ASP1046 4.1 37.1 1.0
C19 B:C522 4.3 28.9 1.0
C15 B:C522 4.4 28.3 1.0
CB B:ILE1044 4.6 32.9 1.0
CA B:ASP1046 4.6 36.9 1.0
CE1 B:HIS1026 4.8 39.4 1.0
CG1 B:VAL898 4.9 37.2 1.0
C20 B:C522 4.9 28.9 1.0
CG B:HIS1026 4.9 40.1 1.0
CA B:ILE1044 4.9 32.9 1.0

Fluorine binding site 6 out of 6 in 3cpc

Go back to Fluorine Binding Sites List in 3cpc
Fluorine binding site 6 out of 6 in the Crystal Structure of the VEGFR2 Kinase Domain in Complex with A Pyridone Inhibitor


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 the VEGFR2 Kinase Domain in Complex with A Pyridone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2

b:31.4
occ:1.00
 F1 B:C522 0.0 31.4 1.0
C21 B:C522 1.3 29.9 1.0
F3 B:C522 2.2 30.3 1.0
F2 B:C522 2.2 30.9 1.0
C17 B:C522 2.3 29.4 1.0
C16 B:C522 2.7 29.1 1.0
CG1 B:VAL898 3.3 37.2 1.0
O B:ILE1044 3.3 32.7 1.0
C18 B:C522 3.6 29.1 1.0
CG1 B:VAL899 3.7 37.7 1.0
C B:ILE1044 4.1 33.1 1.0
C15 B:C522 4.1 28.3 1.0
CD2 B:LEU889 4.1 45.5 1.0
CA B:CYS1045 4.2 34.3 1.0
N B:VAL899 4.3 37.7 1.0
O B:VAL899 4.3 38.8 1.0
N B:CYS1045 4.5 33.5 1.0
CG2 B:ILE1044 4.6 31.8 1.0
C B:CYS1045 4.6 34.7 1.0
CB B:VAL898 4.6 36.9 1.0
C19 B:C522 4.7 28.9 1.0
CB B:VAL899 4.8 38.0 1.0
O1 B:C522 4.8 27.1 1.0
C B:VAL898 4.9 37.1 1.0
CA B:VAL899 4.9 38.1 1.0
CA B:VAL898 4.9 37.0 1.0
C20 B:C522 4.9 28.9 1.0
N B:ASP1046 4.9 35.8 1.0

Reference:

E.Hu, A.Tasker, R.D.White, R.K.Kunz, J.Human, N.Chen, R.Burli, R.Hungate, P.Novak, A.Itano, X.Zhang, V.Yu, Y.Nguyen, Y.Tudor, M.Plant, S.Flynn, Y.Xu, K.L.Meagher, D.A.Whittington, G.Y.Ng. Discovery of Aryl Aminoquinazoline Pyridones As Potent, Selective, and Orally Efficacious Inhibitors of Receptor Tyrosine Kinase C-Kit. J.Med.Chem. V. 51 3065 2008.
ISSN: ISSN 0022-2623
PubMed: 18447379
DOI: 10.1021/JM800188G
Page generated: Wed Jul 31 17:33:20 2024

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