Atomistry » Fluorine » PDB 3b0q-3cct » 3be2
Atomistry »
  Fluorine »
    PDB 3b0q-3cct »
      3be2 »

Fluorine in PDB 3be2: Crystal Structure of the VEGFR2 Kinase Domain in Complex with A Benzamide Inhibitor

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

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

Protein crystallography data

The structure of Crystal Structure of the VEGFR2 Kinase Domain in Complex with A Benzamide Inhibitor, PDB code: 3be2 was solved by D.A.Whittington, J.L.Kim, A.M.Long, Y.Gu, P.Rose, H.Zhao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.00 / 1.75
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 41.770, 84.380, 47.570, 90.00, 100.09, 90.00
R / Rfree (%) 19.7 / 22.6

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the VEGFR2 Kinase Domain in Complex with A Benzamide Inhibitor (pdb code 3be2). 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 Benzamide Inhibitor, PDB code: 3be2:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 3be2

Go back to Fluorine Binding Sites List in 3be2
Fluorine binding site 1 out of 3 in the Crystal Structure of the VEGFR2 Kinase Domain in Complex with A Benzamide 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 Benzamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:22.3
occ:1.00
F2 A:RAJ501 0.0 22.3 1.0
C24 A:RAJ501 1.3 20.7 1.0
F1 A:RAJ501 2.1 22.0 1.0
F3 A:RAJ501 2.1 22.4 1.0
C22 A:RAJ501 2.4 19.2 1.0
C21 A:RAJ501 3.1 19.4 1.0
CD2 A:HIS1026 3.3 17.4 1.0
NE2 A:HIS1026 3.4 17.8 1.0
C23 A:RAJ501 3.4 17.2 1.0
O A:CYS1045 3.6 14.7 1.0
C A:CYS1045 3.6 14.2 1.0
CB A:ASP1046 3.8 16.0 1.0
CG2 A:ILE1044 3.9 15.3 1.0
N A:ASP1046 4.0 15.1 1.0
CA A:CYS1045 4.1 13.5 1.0
O A:HOH79 4.2 24.2 1.0
CD1 A:LEU1019 4.3 14.3 1.0
N A:CYS1045 4.4 13.3 1.0
CA A:ASP1046 4.4 16.8 1.0
CG A:HIS1026 4.4 17.0 1.0
C20 A:RAJ501 4.5 20.2 1.0
CE1 A:HIS1026 4.5 18.2 1.0
O A:ILE1044 4.5 14.3 1.0
C A:ILE1044 4.5 13.6 1.0
C18 A:RAJ501 4.6 17.2 1.0
O A:HOH260 4.8 36.5 1.0
CG A:ASP1046 4.9 17.8 1.0
CB A:ILE1044 4.9 14.3 1.0

Fluorine binding site 2 out of 3 in 3be2

Go back to Fluorine Binding Sites List in 3be2
Fluorine binding site 2 out of 3 in the Crystal Structure of the VEGFR2 Kinase Domain in Complex with A Benzamide 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 Benzamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:22.4
occ:1.00
F3 A:RAJ501 0.0 22.4 1.0
C24 A:RAJ501 1.3 20.7 1.0
F1 A:RAJ501 2.1 22.0 1.0
F2 A:RAJ501 2.1 22.3 1.0
C22 A:RAJ501 2.4 19.2 1.0
C21 A:RAJ501 3.0 19.4 1.0
C23 A:RAJ501 3.6 17.2 1.0
CD1 A:LEU1019 3.8 14.3 1.0
CD2 A:LEU1019 3.9 14.6 1.0
CD1 A:ILE892 4.0 18.7 1.0
CG1 A:VAL898 4.1 15.3 1.0
C20 A:RAJ501 4.4 20.2 1.0
O A:HOH260 4.5 36.5 1.0
CG A:LEU1019 4.5 14.2 1.0
C18 A:RAJ501 4.8 17.2 1.0
CD2 A:LEU889 4.8 16.0 1.0
CD2 A:HIS1026 5.0 17.4 1.0
O A:ILE1044 5.0 14.3 1.0
CG2 A:ILE1044 5.0 15.3 1.0

Fluorine binding site 3 out of 3 in 3be2

Go back to Fluorine Binding Sites List in 3be2
Fluorine binding site 3 out of 3 in the Crystal Structure of the VEGFR2 Kinase Domain in Complex with A Benzamide 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 Benzamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:22.0
occ:1.00
F1 A:RAJ501 0.0 22.0 1.0
C24 A:RAJ501 1.3 20.7 1.0
F2 A:RAJ501 2.1 22.3 1.0
F3 A:RAJ501 2.1 22.4 1.0
C22 A:RAJ501 2.4 19.2 1.0
C23 A:RAJ501 2.8 17.2 1.0
O A:ILE1044 3.0 14.3 1.0
CA A:CYS1045 3.6 13.5 1.0
C A:ILE1044 3.6 13.6 1.0
CG1 A:VAL898 3.7 15.3 1.0
C21 A:RAJ501 3.7 19.4 1.0
N A:CYS1045 3.9 13.3 1.0
C A:CYS1045 3.9 14.2 1.0
CG2 A:ILE1044 4.1 15.3 1.0
C18 A:RAJ501 4.3 17.2 1.0
CG1 A:VAL899 4.3 15.3 1.0
N A:ASP1046 4.3 15.1 1.0
O A:CYS1045 4.4 14.7 1.0
CB A:ILE1044 4.5 14.3 1.0
O1 A:RAJ501 4.5 14.3 1.0
CA A:ILE1044 4.7 13.8 1.0
N A:VAL899 4.8 13.2 1.0
CB A:VAL898 4.8 14.3 1.0
CD1 A:LEU1019 4.8 14.3 1.0
C20 A:RAJ501 4.9 20.2 1.0
CB A:CYS1045 5.0 12.4 1.0
CA A:VAL898 5.0 13.1 1.0

Reference:

J.C.Harmange, M.M.Weiss, J.Germain, A.J.Polverino, G.Borg, J.Bready, D.Chen, D.Choquette, A.Coxon, T.Demelfi, L.Dipietro, N.Doerr, J.Estrada, J.Flynn, R.F.Graceffa, S.P.Harriman, S.Kaufman, D.S.La, A.Long, M.W.Martin, S.Neervannan, V.F.Patel, M.Potashman, K.Regal, P.M.Roveto, M.L.Schrag, C.Starnes, A.Tasker, Y.Teffera, L.Wang, R.D.White, D.A.Whittington, R.Zanon. Naphthamides As Novel and Potent Vascular Endothelial Growth Factor Receptor Tyrosine Kinase Inhibitors: Design, Synthesis, and Evaluation. J.Med.Chem. V. 51 1649 2008.
ISSN: ISSN 0022-2623
PubMed: 18324761
DOI: 10.1021/JM701097Z
Page generated: Sun Dec 13 11:43:22 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy