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Fluorine in PDB 4agd: Crystal Structure of VEGFR2 (Juxtamembrane and Kinase Domains) in Complex with Sunitinib (SU11248) (N-2-Diethylaminoethyl)-5-((Z)-(5- Fluoro-2-Oxo-1H-Indol-3-Ylidene)Methyl)-2,4-Dimethyl-1H-Pyrrole-3- Carboxamide)

Enzymatic activity of Crystal Structure of VEGFR2 (Juxtamembrane and Kinase Domains) in Complex with Sunitinib (SU11248) (N-2-Diethylaminoethyl)-5-((Z)-(5- Fluoro-2-Oxo-1H-Indol-3-Ylidene)Methyl)-2,4-Dimethyl-1H-Pyrrole-3- Carboxamide)

All present enzymatic activity of Crystal Structure of VEGFR2 (Juxtamembrane and Kinase Domains) in Complex with Sunitinib (SU11248) (N-2-Diethylaminoethyl)-5-((Z)-(5- Fluoro-2-Oxo-1H-Indol-3-Ylidene)Methyl)-2,4-Dimethyl-1H-Pyrrole-3- Carboxamide):
2.7.10.1;

Protein crystallography data

The structure of Crystal Structure of VEGFR2 (Juxtamembrane and Kinase Domains) in Complex with Sunitinib (SU11248) (N-2-Diethylaminoethyl)-5-((Z)-(5- Fluoro-2-Oxo-1H-Indol-3-Ylidene)Methyl)-2,4-Dimethyl-1H-Pyrrole-3- Carboxamide), PDB code: 4agd was solved by M.Mctigue, Y.Deng, K.Ryan, A.Brooun, W.Diehl, A.Stewart, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.69 / 2.81
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 134.694, 56.980, 52.720, 90.00, 94.34, 90.00
R / Rfree (%) 21 / 30.7

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of VEGFR2 (Juxtamembrane and Kinase Domains) in Complex with Sunitinib (SU11248) (N-2-Diethylaminoethyl)-5-((Z)-(5- Fluoro-2-Oxo-1H-Indol-3-Ylidene)Methyl)-2,4-Dimethyl-1H-Pyrrole-3- Carboxamide) (pdb code 4agd). 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 VEGFR2 (Juxtamembrane and Kinase Domains) in Complex with Sunitinib (SU11248) (N-2-Diethylaminoethyl)-5-((Z)-(5- Fluoro-2-Oxo-1H-Indol-3-Ylidene)Methyl)-2,4-Dimethyl-1H-Pyrrole-3- Carboxamide), PDB code: 4agd:

Fluorine binding site 1 out of 1 in 4agd

Go back to Fluorine Binding Sites List in 4agd
Fluorine binding site 1 out of 1 in the Crystal Structure of VEGFR2 (Juxtamembrane and Kinase Domains) in Complex with Sunitinib (SU11248) (N-2-Diethylaminoethyl)-5-((Z)-(5- Fluoro-2-Oxo-1H-Indol-3-Ylidene)Methyl)-2,4-Dimethyl-1H-Pyrrole-3- Carboxamide)


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 VEGFR2 (Juxtamembrane and Kinase Domains) in Complex with Sunitinib (SU11248) (N-2-Diethylaminoethyl)-5-((Z)-(5- Fluoro-2-Oxo-1H-Indol-3-Ylidene)Methyl)-2,4-Dimethyl-1H-Pyrrole-3- Carboxamide) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2000

b:48.6
occ:1.00
 F29 A:B492000 0.0 48.6 1.0
C15 A:B492000 1.3 46.9 1.0
C5 A:B492000 2.4 46.9 1.0
C7 A:B492000 2.4 45.3 1.0
NZ A:LYS868 3.0 43.4 1.0
O A:ASP1046 3.1 40.0 1.0
CA A:PHE1047 3.2 43.9 1.0
C A:ASP1046 3.3 42.4 1.0
N A:PHE1047 3.4 43.6 1.0
CE A:LYS868 3.4 43.9 1.0
C6 A:B492000 3.7 43.2 1.0
C17 A:B492000 3.7 43.9 1.0
CB A:CYS1045 4.0 40.9 1.0
N A:ASP1046 4.1 42.1 1.0
C A:PHE1047 4.1 43.9 1.0
SG A:CYS1045 4.1 45.2 1.0
CG A:PHE1047 4.1 43.5 1.0
CD1 A:PHE1047 4.1 42.8 1.0
O A:HOH2054 4.1 42.2 1.0
C16 A:B492000 4.2 41.2 1.0
CB A:PHE1047 4.3 43.9 1.0
O A:PHE1047 4.3 44.9 1.0
CA A:ASP1046 4.4 43.2 1.0
CG2 A:VAL848 4.4 55.1 1.0
CD2 A:PHE1047 4.6 41.8 1.0
CE1 A:PHE1047 4.6 41.2 1.0
C A:CYS1045 4.8 42.1 1.0
CD A:LYS868 4.8 43.8 1.0
CA A:CYS1045 5.0 41.7 1.0

Reference:

M.Mctigue, B.W.Murray, J.H.Chen, Y.Deng, J.Solowiej, R.S.Kania. Molecular Conformations, Interactions, and Properties Associated with Drug Efficiency and Clinical Performance Among Vegfr Tk Inhibitors. Proc.Natl.Acad.Sci.Usa V. 109 18281 2012.
ISSN: ISSN 0027-8424
PubMed: 22988103
DOI: 10.1073/PNAS.1207759109
Page generated: Wed Jul 31 23:58:33 2024

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