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Fluorine in PDB 5ew3: Human Vascular Endothelial Growth Factor Receptor 2 (Kdr) Kinase Domain in Complex with AAL993

Enzymatic activity of Human Vascular Endothelial Growth Factor Receptor 2 (Kdr) Kinase Domain in Complex with AAL993

All present enzymatic activity of Human Vascular Endothelial Growth Factor Receptor 2 (Kdr) Kinase Domain in Complex with AAL993:
2.7.10.1;

Protein crystallography data

The structure of Human Vascular Endothelial Growth Factor Receptor 2 (Kdr) Kinase Domain in Complex with AAL993, PDB code: 5ew3 was solved by W.Stark, A.Goepfert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.68 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 67.500, 55.760, 89.760, 90.00, 92.28, 90.00
R / Rfree (%) 21.8 / 25.4

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Human Vascular Endothelial Growth Factor Receptor 2 (Kdr) Kinase Domain in Complex with AAL993 (pdb code 5ew3). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Human Vascular Endothelial Growth Factor Receptor 2 (Kdr) Kinase Domain in Complex with AAL993, PDB code: 5ew3:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5ew3

Go back to Fluorine Binding Sites List in 5ew3
Fluorine binding site 1 out of 6 in the Human Vascular Endothelial Growth Factor Receptor 2 (Kdr) Kinase Domain in Complex with AAL993


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human Vascular Endothelial Growth Factor Receptor 2 (Kdr) Kinase Domain in Complex with AAL993 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1201

b:46.0
occ:1.00
 F25 A:5T21201 0.0 46.0 1.0
C24 A:5T21201 1.4 43.0 1.0
F26 A:5T21201 2.2 47.0 1.0
F27 A:5T21201 2.2 40.9 1.0
C13 A:5T21201 2.4 41.2 1.0
C14 A:5T21201 2.8 40.8 1.0
CD1 A:LEU1019 3.6 43.5 1.0
C12 A:5T21201 3.7 41.6 1.0
CD2 A:LEU1019 3.7 44.0 1.0
CD1 A:ILE892 3.8 63.1 1.0
CD2 A:HIS1026 4.2 46.0 1.0
C15 A:5T21201 4.2 39.7 1.0
CG A:LEU1019 4.3 43.7 1.0
CG1 A:VAL898 4.3 44.6 1.0
NE2 A:HIS1026 4.5 45.7 1.0
CG2 A:ILE1044 4.8 36.8 1.0
C11 A:5T21201 4.8 40.0 1.0
O A:HOH1302 4.9 49.2 1.0
O A:ILE1044 5.0 38.0 1.0

Fluorine binding site 2 out of 6 in 5ew3

Go back to Fluorine Binding Sites List in 5ew3
Fluorine binding site 2 out of 6 in the Human Vascular Endothelial Growth Factor Receptor 2 (Kdr) Kinase Domain in Complex with AAL993


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human Vascular Endothelial Growth Factor Receptor 2 (Kdr) Kinase Domain in Complex with AAL993 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1201

b:47.0
occ:1.00
 F26 A:5T21201 0.0 47.0 1.0
C24 A:5T21201 1.3 43.0 1.0
F25 A:5T21201 2.2 46.0 1.0
F27 A:5T21201 2.2 40.9 1.0
C13 A:5T21201 2.3 41.2 1.0
C12 A:5T21201 3.1 41.6 1.0
NE2 A:HIS1026 3.2 45.7 1.0
C14 A:5T21201 3.2 40.8 1.0
C A:CYS1045 3.2 39.1 1.0
O A:CYS1045 3.3 37.9 1.0
CA A:CYS1045 3.4 36.5 1.0
CD2 A:HIS1026 3.4 46.0 1.0
N A:CYS1045 3.5 36.0 1.0
CG2 A:ILE1044 3.6 36.8 1.0
C A:ILE1044 3.7 38.9 1.0
O A:ILE1044 3.7 38.0 1.0
N A:ASP1046 3.8 35.8 1.0
CB A:ASP1046 4.3 38.6 1.0
C11 A:5T21201 4.3 40.0 1.0
CE1 A:HIS1026 4.4 45.3 1.0
CB A:ILE1044 4.4 37.2 1.0
C15 A:5T21201 4.4 39.7 1.0
CA A:ASP1046 4.6 36.5 1.0
CA A:ILE1044 4.6 34.6 1.0
CD1 A:LEU1019 4.7 43.5 1.0
CG A:HIS1026 4.7 44.9 1.0
CB A:CYS1045 4.8 37.5 1.0
C16 A:5T21201 4.9 39.6 1.0
O10 A:5T21201 5.0 42.4 1.0

Fluorine binding site 3 out of 6 in 5ew3

Go back to Fluorine Binding Sites List in 5ew3
Fluorine binding site 3 out of 6 in the Human Vascular Endothelial Growth Factor Receptor 2 (Kdr) Kinase Domain in Complex with AAL993


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human Vascular Endothelial Growth Factor Receptor 2 (Kdr) Kinase Domain in Complex with AAL993 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1201

b:40.9
occ:1.00
 F27 A:5T21201 0.0 40.9 1.0
C24 A:5T21201 1.3 43.0 1.0
F26 A:5T21201 2.2 47.0 1.0
F25 A:5T21201 2.2 46.0 1.0
C13 A:5T21201 2.3 41.2 1.0
C12 A:5T21201 2.8 41.6 1.0
CG1 A:VAL898 3.3 44.6 1.0
O A:ILE1044 3.4 38.0 1.0
C14 A:5T21201 3.6 40.8 1.0
CG1 A:VAL899 3.8 50.6 1.0
C A:ILE1044 4.0 38.9 1.0
CA A:CYS1045 4.1 36.5 1.0
C11 A:5T21201 4.1 40.0 1.0
N A:VAL899 4.3 45.9 1.0
CD2 A:LEU889 4.3 51.1 1.0
N A:CYS1045 4.4 36.0 1.0
O A:VAL899 4.5 51.1 1.0
C A:CYS1045 4.6 39.1 1.0
CB A:VAL898 4.7 45.4 1.0
CD1 A:ILE892 4.7 63.1 1.0
C15 A:5T21201 4.7 39.7 1.0
CG2 A:ILE1044 4.8 36.8 1.0
CB A:VAL899 4.9 51.0 1.0
O10 A:5T21201 4.9 42.4 1.0
CA A:VAL898 4.9 42.0 1.0
C16 A:5T21201 4.9 39.6 1.0
CD2 A:LEU1019 5.0 44.0 1.0
N A:ASP1046 5.0 35.8 1.0
CA A:VAL899 5.0 46.5 1.0

Fluorine binding site 4 out of 6 in 5ew3

Go back to Fluorine Binding Sites List in 5ew3
Fluorine binding site 4 out of 6 in the Human Vascular Endothelial Growth Factor Receptor 2 (Kdr) Kinase Domain in Complex with AAL993


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Human Vascular Endothelial Growth Factor Receptor 2 (Kdr) Kinase Domain in Complex with AAL993 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1201

b:55.4
occ:1.00
 F25 B:5T21201 0.0 55.4 1.0
C24 B:5T21201 1.4 55.6 1.0
F27 B:5T21201 2.2 55.7 1.0
F26 B:5T21201 2.2 54.7 1.0
C13 B:5T21201 2.4 57.3 1.0
C14 B:5T21201 2.9 59.0 1.0
CD1 B:ILE892 3.5 69.0 1.0
CD2 B:LEU1019 3.5 61.1 1.0
C12 B:5T21201 3.6 57.0 1.0
CD1 B:LEU1019 3.8 60.6 1.0
CG1 B:VAL898 3.9 47.9 1.0
CG B:LEU1019 4.3 59.7 1.0
C15 B:5T21201 4.3 59.9 1.0
CG1 B:ILE892 4.7 65.4 1.0
CD2 B:HIS1026 4.7 74.2 1.0
C11 B:5T21201 4.8 57.0 1.0
O B:ILE1044 4.9 51.9 1.0
CD2 B:LEU889 4.9 61.9 1.0

Fluorine binding site 5 out of 6 in 5ew3

Go back to Fluorine Binding Sites List in 5ew3
Fluorine binding site 5 out of 6 in the Human Vascular Endothelial Growth Factor Receptor 2 (Kdr) Kinase Domain in Complex with AAL993


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Human Vascular Endothelial Growth Factor Receptor 2 (Kdr) Kinase Domain in Complex with AAL993 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1201

b:54.7
occ:1.00
 F26 B:5T21201 0.0 54.7 1.0
C24 B:5T21201 1.4 55.6 1.0
F25 B:5T21201 2.2 55.4 1.0
F27 B:5T21201 2.2 55.7 1.0
C13 B:5T21201 2.3 57.3 1.0
C14 B:5T21201 3.1 59.0 1.0
NE2 B:HIS1026 3.2 73.9 1.0
C12 B:5T21201 3.3 57.0 1.0
CD2 B:HIS1026 3.4 74.2 1.0
C B:CYS1045 3.5 54.6 1.0
CG2 B:ILE1044 3.6 51.4 1.0
O B:CYS1045 3.6 52.6 1.0
CA B:CYS1045 3.6 51.7 1.0
N B:CYS1045 3.7 51.5 1.0
O B:ILE1044 3.8 51.9 1.0
C B:ILE1044 3.8 53.0 1.0
N B:ASP1046 4.1 52.8 1.0
CB B:ILE1044 4.4 50.9 1.0
CD1 B:LEU1019 4.4 60.6 1.0
C15 B:5T21201 4.4 59.9 1.0
CE1 B:HIS1026 4.5 73.6 1.0
C11 B:5T21201 4.5 57.0 1.0
CB B:ASP1046 4.5 56.0 1.0
CG B:HIS1026 4.6 72.9 1.0
CA B:ILE1044 4.7 47.9 1.0
CG1 B:VAL898 4.8 47.9 1.0
CA B:ASP1046 4.9 53.9 1.0
C16 B:5T21201 4.9 59.0 1.0

Fluorine binding site 6 out of 6 in 5ew3

Go back to Fluorine Binding Sites List in 5ew3
Fluorine binding site 6 out of 6 in the Human Vascular Endothelial Growth Factor Receptor 2 (Kdr) Kinase Domain in Complex with AAL993


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Human Vascular Endothelial Growth Factor Receptor 2 (Kdr) Kinase Domain in Complex with AAL993 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1201

b:55.7
occ:1.00
 F27 B:5T21201 0.0 55.7 1.0
C24 B:5T21201 1.4 55.6 1.0
F25 B:5T21201 2.2 55.4 1.0
F26 B:5T21201 2.2 54.7 1.0
C13 B:5T21201 2.4 57.3 1.0
C12 B:5T21201 2.7 57.0 1.0
O B:ILE1044 3.2 51.9 1.0
CG1 B:VAL898 3.4 47.9 1.0
CG2 B:VAL899 3.5 52.2 1.0
C14 B:5T21201 3.7 59.0 1.0
C B:ILE1044 3.9 53.0 1.0
CA B:CYS1045 4.0 51.7 1.0
C11 B:5T21201 4.1 57.0 1.0
N B:VAL899 4.1 47.2 1.0
N B:CYS1045 4.3 51.5 1.0
CD2 B:LEU889 4.3 61.9 1.0
O B:VAL899 4.4 51.5 1.0
C B:CYS1045 4.5 54.6 1.0
O10 B:5T21201 4.6 54.5 1.0
CB B:VAL898 4.7 48.1 1.0
CB B:VAL899 4.7 52.5 1.0
CA B:VAL899 4.8 47.9 1.0
C15 B:5T21201 4.8 59.9 1.0
N B:ASP1046 4.9 52.8 1.0
CD1 B:ILE892 4.9 69.0 1.0
CA B:VAL898 4.9 44.5 1.0
C B:VAL898 4.9 48.9 1.0
C16 B:5T21201 4.9 59.0 1.0
N9 B:5T21201 4.9 54.9 1.0
CG2 B:ILE1044 4.9 51.4 1.0

Reference:

G.Bold, C.Schnell, P.Furet, P.Mcsheehy, J.Bruggen, J.Mestan, P.W.Manley, P.Druckes, M.Burglin, U.Durler, J.Loretan, R.Reuter, M.Wartmann, A.Theuer, B.Bauer-Probst, G.Martiny-Baron, P.Allegrini, A.Goepfert, J.Wood, A.Littlewood-Evans. A Novel Potent Oral Series of VEGFR2 Inhibitors Abrogate Tumor Growth By Inhibiting Angiogenesis. J.Med.Chem. V. 59 132 2016.
ISSN: ISSN 0022-2623
PubMed: 26629594
DOI: 10.1021/ACS.JMEDCHEM.5B01582
Page generated: Thu Aug 1 09:15:12 2024

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