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Fluorine in PDB 4asd: Crystal Structure of VEGFR2 (Juxtamembrane and Kinase Domains) in Complex with Sorafenib (Bay 43-9006)

Enzymatic activity of Crystal Structure of VEGFR2 (Juxtamembrane and Kinase Domains) in Complex with Sorafenib (Bay 43-9006)

All present enzymatic activity of Crystal Structure of VEGFR2 (Juxtamembrane and Kinase Domains) in Complex with Sorafenib (Bay 43-9006):
2.7.10.1;

Protein crystallography data

The structure of Crystal Structure of VEGFR2 (Juxtamembrane and Kinase Domains) in Complex with Sorafenib (Bay 43-9006), PDB code: 4asd 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) 15.00 / 2.03
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 135.818, 56.479, 52.052, 90.00, 95.42, 90.00
R / Rfree (%) 17.5 / 23

Other elements in 4asd:

The structure of Crystal Structure of VEGFR2 (Juxtamembrane and Kinase Domains) in Complex with Sorafenib (Bay 43-9006) also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of VEGFR2 (Juxtamembrane and Kinase Domains) in Complex with Sorafenib (Bay 43-9006) (pdb code 4asd). 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 VEGFR2 (Juxtamembrane and Kinase Domains) in Complex with Sorafenib (Bay 43-9006), PDB code: 4asd:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 4asd

Go back to Fluorine Binding Sites List in 4asd
Fluorine binding site 1 out of 3 in the Crystal Structure of VEGFR2 (Juxtamembrane and Kinase Domains) in Complex with Sorafenib (Bay 43-9006)


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 Sorafenib (Bay 43-9006) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1500

b:28.9
occ:1.00
F8 A:BAX1500 0.0 28.9 1.0
C7 A:BAX1500 1.4 28.4 1.0
F10 A:BAX1500 2.1 28.7 1.0
F9 A:BAX1500 2.2 29.6 1.0
C6 A:BAX1500 2.4 27.9 1.0
C5 A:BAX1500 3.0 29.0 1.0
CL11 A:BAX1500 3.1 33.6 1.0
CD2 A:HIS1026 3.4 21.1 1.0
CG2 A:ILE1044 3.4 20.4 1.0
C1 A:BAX1500 3.4 28.1 1.0
CD1 A:LEU1019 3.5 25.9 1.0
NE2 A:HIS1026 3.7 20.7 1.0
C A:CYS1045 4.2 17.5 1.0
O A:CYS1045 4.2 17.8 1.0
CA A:CYS1045 4.3 17.7 1.0
C4 A:BAX1500 4.4 28.4 1.0
N A:CYS1045 4.4 17.6 1.0
C A:ILE1044 4.4 18.0 1.0
CB A:ILE1044 4.4 18.9 1.0
CG A:HIS1026 4.5 22.9 1.0
CD2 A:LEU1019 4.5 24.5 1.0
O A:ILE1044 4.5 17.3 1.0
C2 A:BAX1500 4.6 26.8 1.0
CG A:LEU1019 4.6 25.8 1.0
N A:ASP1046 4.7 17.9 1.0
CE1 A:HIS1026 4.9 21.4 1.0
CB A:ASP1046 4.9 18.8 1.0
C3 A:BAX1500 5.0 27.7 1.0

Fluorine binding site 2 out of 3 in 4asd

Go back to Fluorine Binding Sites List in 4asd
Fluorine binding site 2 out of 3 in the Crystal Structure of VEGFR2 (Juxtamembrane and Kinase Domains) in Complex with Sorafenib (Bay 43-9006)


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 VEGFR2 (Juxtamembrane and Kinase Domains) in Complex with Sorafenib (Bay 43-9006) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1500

b:29.6
occ:1.00
F9 A:BAX1500 0.0 29.6 1.0
C7 A:BAX1500 1.4 28.4 1.0
F10 A:BAX1500 2.2 28.7 1.0
F8 A:BAX1500 2.2 28.9 1.0
C6 A:BAX1500 2.4 27.9 1.0
C5 A:BAX1500 3.1 29.0 1.0
CL11 A:BAX1500 3.1 33.6 1.0
CD2 A:LEU1019 3.3 24.5 1.0
C1 A:BAX1500 3.5 28.1 1.0
CD1 A:LEU1019 3.7 25.9 1.0
CD1 A:ILE892 4.0 23.9 1.0
CG A:LEU1019 4.1 25.8 1.0
C4 A:BAX1500 4.4 28.4 1.0
CD2 A:LEU889 4.5 21.7 1.0
CB A:VAL898 4.6 20.4 1.0
C2 A:BAX1500 4.7 26.8 1.0
CG2 A:ILE892 4.9 23.3 1.0
CG2 A:ILE1044 4.9 20.4 1.0
CG1 A:VAL898 4.9 19.5 1.0
O A:ILE1044 4.9 17.3 1.0

Fluorine binding site 3 out of 3 in 4asd

Go back to Fluorine Binding Sites List in 4asd
Fluorine binding site 3 out of 3 in the Crystal Structure of VEGFR2 (Juxtamembrane and Kinase Domains) in Complex with Sorafenib (Bay 43-9006)


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 VEGFR2 (Juxtamembrane and Kinase Domains) in Complex with Sorafenib (Bay 43-9006) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1500

b:28.7
occ:1.00
F10 A:BAX1500 0.0 28.7 1.0
C7 A:BAX1500 1.4 28.4 1.0
F8 A:BAX1500 2.1 28.9 1.0
F9 A:BAX1500 2.2 29.6 1.0
C6 A:BAX1500 2.4 27.9 1.0
C1 A:BAX1500 2.7 28.1 1.0
O A:ILE1044 3.0 17.3 1.0
CA A:CYS1045 3.5 17.7 1.0
C A:ILE1044 3.5 18.0 1.0
C5 A:BAX1500 3.7 29.0 1.0
N A:CYS1045 3.8 17.6 1.0
CG2 A:ILE1044 4.0 20.4 1.0
CG1 A:VAL899 4.0 21.9 1.0
C A:CYS1045 4.1 17.5 1.0
C2 A:BAX1500 4.2 26.8 1.0
O15 A:BAX1500 4.2 16.6 1.0
N A:VAL899 4.3 19.8 1.0
CB A:ILE1044 4.4 18.9 1.0
CL11 A:BAX1500 4.5 33.6 1.0
CB A:VAL898 4.5 20.4 1.0
N A:ASP1046 4.5 17.9 1.0
CA A:ILE1044 4.6 18.3 1.0
O A:CYS1045 4.6 17.8 1.0
CB A:CYS1045 4.7 16.6 1.0
CD1 A:LEU1019 4.8 25.9 1.0
CA A:VAL898 4.8 19.7 1.0
C4 A:BAX1500 4.9 28.4 1.0
CD2 A:LEU889 4.9 21.7 1.0
O A:VAL899 4.9 21.0 1.0
CB A:VAL899 5.0 20.8 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: Sun Dec 13 11:58:55 2020

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