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Fluorine in PDB 2qu5: Crystal Structure of the VEGFR2 Kinase Domain in Complex with A Benzimidazole Inhibitor

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

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

Protein crystallography data

The structure of Crystal Structure of the VEGFR2 Kinase Domain in Complex with A Benzimidazole Inhibitor, PDB code: 2qu5 was solved by D.A.Whittington, J.L.Kim, 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 / 2.95
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 66.852, 143.828, 58.483, 90.00, 90.00, 90.00
R / Rfree (%) 21.3 / 25.1

Other elements in 2qu5:

The structure of Crystal Structure of the VEGFR2 Kinase Domain in Complex with A Benzimidazole Inhibitor also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the VEGFR2 Kinase Domain in Complex with A Benzimidazole Inhibitor (pdb code 2qu5). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of the VEGFR2 Kinase Domain in Complex with A Benzimidazole Inhibitor, PDB code: 2qu5:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 2qu5

Go back to Fluorine Binding Sites List in 2qu5
Fluorine binding site 1 out of 3 in the Crystal Structure of the VEGFR2 Kinase Domain in Complex with A Benzimidazole 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 Benzimidazole Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:55.4
occ:1.00
F45 A:276501 0.0 55.4 1.0
C43 A:276501 1.3 56.2 1.0
F46 A:276501 2.2 56.4 1.0
F47 A:276501 2.2 57.5 1.0
C35 A:276501 2.3 55.2 1.0
C36 A:276501 3.0 54.9 1.0
C34 A:276501 3.3 53.0 1.0
CD1 A:ILE892 3.3 50.5 1.0
CL44 A:276501 3.3 56.8 1.0
CG2 A:ILE888 3.6 50.5 1.0
CD2 A:LEU889 4.1 53.1 1.0
C37 A:276501 4.3 53.9 1.0
CB A:ILE888 4.4 52.2 1.0
C33 A:276501 4.5 52.0 1.0
CG A:LEU889 4.6 52.8 1.0
CG1 A:ILE892 4.7 52.6 1.0
N A:LEU889 4.8 51.5 1.0
C38 A:276501 4.9 52.4 1.0

Fluorine binding site 2 out of 3 in 2qu5

Go back to Fluorine Binding Sites List in 2qu5
Fluorine binding site 2 out of 3 in the Crystal Structure of the VEGFR2 Kinase Domain in Complex with A Benzimidazole 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 Benzimidazole Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:56.4
occ:1.00
F46 A:276501 0.0 56.4 1.0
C43 A:276501 1.3 56.2 1.0
F47 A:276501 2.2 57.5 1.0
F45 A:276501 2.2 55.4 1.0
C35 A:276501 2.3 55.2 1.0
C36 A:276501 3.0 54.9 1.0
CL44 A:276501 3.1 56.8 1.0
C34 A:276501 3.5 53.0 1.0
CA A:HIS1026 3.8 55.8 1.0
CD2 A:HIS1026 3.9 57.1 1.0
O A:ILE1025 4.1 59.3 1.0
CG A:HIS1026 4.2 57.9 1.0
O A:HIS1026 4.3 54.9 1.0
C37 A:276501 4.3 53.9 1.0
CB A:HIS1026 4.3 57.4 1.0
CD2 A:LEU1019 4.4 42.1 1.0
C A:HIS1026 4.6 54.0 1.0
NE2 A:HIS1026 4.6 59.2 1.0
N A:HIS1026 4.7 57.1 1.0
C33 A:276501 4.7 52.0 1.0
C A:ILE1025 4.7 57.3 1.0
CD1 A:ILE892 5.0 50.5 1.0

Fluorine binding site 3 out of 3 in 2qu5

Go back to Fluorine Binding Sites List in 2qu5
Fluorine binding site 3 out of 3 in the Crystal Structure of the VEGFR2 Kinase Domain in Complex with A Benzimidazole 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 Benzimidazole Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:57.5
occ:1.00
F47 A:276501 0.0 57.5 1.0
C43 A:276501 1.3 56.2 1.0
F46 A:276501 2.2 56.4 1.0
F45 A:276501 2.2 55.4 1.0
C35 A:276501 2.4 55.2 1.0
C34 A:276501 2.7 53.0 1.0
C36 A:276501 3.7 54.9 1.0
C33 A:276501 4.1 52.0 1.0
CG A:GLU885 4.4 63.7 1.0
CL44 A:276501 4.6 56.8 1.0
CG2 A:ILE888 4.7 50.5 1.0
N32 A:276501 4.8 50.9 1.0
C37 A:276501 4.8 53.9 1.0
OD1 A:ASP1046 4.9 54.3 1.0
O A:HIS1026 4.9 54.9 1.0
C38 A:276501 5.0 52.4 1.0

Reference:

M.H.Potashman, J.Bready, A.Coxon, T.M.Demelfi, L.Dipietro, N.Doerr, D.Elbaum, J.Estrada, P.Gallant, J.Germain, Y.Gu, J.C.Harmange, S.A.Kaufman, R.Kendall, J.L.Kim, G.N.Kumar, A.M.Long, S.Neervannan, V.F.Patel, A.Polverino, P.Rose, S.V.Plas, D.Whittington, R.Zanon, H.Zhao. Design, Synthesis, and Evaluation of Orally Active Benzimidazoles and Benzoxazoles As Vascular Endothelial Growth Factor-2 Receptor Tyrosine Kinase Inhibitors. J.Med.Chem. V. 50 4351 2007.
ISSN: ISSN 0022-2623
PubMed: 17696416
DOI: 10.1021/JM070034I
Page generated: Sun Dec 13 11:39:40 2020

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