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Fluorine in PDB 3vnt: Crystal Structure of the Kinase Domain of Human VEGFR2 with A [1, 3]Thiazolo[5,4-B]Pyridine Derivative

Enzymatic activity of Crystal Structure of the Kinase Domain of Human VEGFR2 with A [1, 3]Thiazolo[5,4-B]Pyridine Derivative

All present enzymatic activity of Crystal Structure of the Kinase Domain of Human VEGFR2 with A [1, 3]Thiazolo[5,4-B]Pyridine Derivative:
2.7.10.1;

Protein crystallography data

The structure of Crystal Structure of the Kinase Domain of Human VEGFR2 with A [1, 3]Thiazolo[5,4-B]Pyridine Derivative, PDB code: 3vnt was solved by H.Oki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.33 / 1.64
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 135.615, 56.618, 51.819, 90.00, 94.88, 90.00
R / Rfree (%) 15.1 / 19.2

Other elements in 3vnt:

The structure of Crystal Structure of the Kinase Domain of Human VEGFR2 with A [1, 3]Thiazolo[5,4-B]Pyridine Derivative 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 Kinase Domain of Human VEGFR2 with A [1, 3]Thiazolo[5,4-B]Pyridine Derivative (pdb code 3vnt). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total only one binding site of Fluorine was determined in the Crystal Structure of the Kinase Domain of Human VEGFR2 with A [1, 3]Thiazolo[5,4-B]Pyridine Derivative, PDB code: 3vnt:

Fluorine binding site 1 out of 1 in 3vnt

Go back to Fluorine Binding Sites List in 3vnt
Fluorine binding site 1 out of 1 in the Crystal Structure of the Kinase Domain of Human VEGFR2 with A [1, 3]Thiazolo[5,4-B]Pyridine Derivative


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 Kinase Domain of Human VEGFR2 with A [1, 3]Thiazolo[5,4-B]Pyridine Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2001

b:17.3
occ:1.00
 F1 A:0JA2001 0.0 17.3 1.0
C2 A:0JA2001 1.4 16.6 1.0
C23 A:0JA2001 2.3 19.0 1.0
C3 A:0JA2001 2.4 17.4 1.0
N24 A:0JA2001 2.6 18.6 1.0
OE2 A:GLU885 3.2 22.4 1.0
CG1 A:VAL914 3.3 17.6 1.0
CG1 A:VAL916 3.3 17.6 1.0
CD1 A:LEU889 3.6 20.0 1.0
C22 A:0JA2001 3.6 17.5 1.0
C4 A:0JA2001 3.6 17.5 1.0
C25 A:0JA2001 3.9 18.9 1.0
CB A:VAL914 3.9 16.0 1.0
C5 A:0JA2001 4.1 15.8 1.0
O A:VAL914 4.2 16.9 1.0
CB A:LYS868 4.2 17.1 1.0
CD A:GLU885 4.3 22.3 1.0
CG2 A:VAL916 4.5 18.2 1.0
CB A:VAL916 4.5 16.9 1.0
CE A:LYS868 4.5 20.3 1.0
CD A:LYS868 4.6 18.4 1.0
C A:VAL914 4.6 17.2 1.0
NZ A:LYS868 4.6 21.8 1.0
O26 A:0JA2001 4.7 20.7 1.0
C27 A:0JA2001 4.8 19.7 1.0
CG A:GLU885 4.8 21.7 1.0
CA A:VAL914 4.9 16.4 1.0
C28 A:0JA2001 5.0 24.3 1.0

Reference:

M.Okaniwa, M.Hirose, T.Imada, T.Ohashi, Y.Hayashi, T.Miyazaki, T.Arita, M.Yabuki, K.Kakoi, J.Kato, T.Takagi, T.Kawamoto, S.Yao, A.Sumita, S.Tsutsumi, T.Tottori, H.Oki, B.C.Sang, J.Yano, K.Aertgeerts, S.Yoshida, T.Ishikawa. Design and Synthesis of Novel Dfg-Out Raf/Vascular Endothelial Growth Factor Receptor 2 (VEGFR2) Inhibitors. 1. Exploration of [5,6]-Fused Bicyclic Scaffolds J.Med.Chem. V. 55 3452 2012.
ISSN: ISSN 0022-2623
PubMed: 22376051
DOI: 10.1021/JM300126X
Page generated: Mon Jul 14 19:54:08 2025

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