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Fluorine in PDB 3vhe: Crystal Structure of Human VEGFR2 Kinase Domain with A Novel Pyrrolopyrimidine Inhibitor.

Enzymatic activity of Crystal Structure of Human VEGFR2 Kinase Domain with A Novel Pyrrolopyrimidine Inhibitor.

All present enzymatic activity of Crystal Structure of Human VEGFR2 Kinase Domain with A Novel Pyrrolopyrimidine Inhibitor.:
2.7.10.1;

Protein crystallography data

The structure of Crystal Structure of Human VEGFR2 Kinase Domain with A Novel Pyrrolopyrimidine Inhibitor., PDB code: 3vhe was solved by Y.Oguro, N.Miyamoto, K.Okada, T.Takagi, H.Iwata, Y.Awazu, H.Miki, A.Hori, K.Kamiyama, S.Imanura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.84 / 1.55
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 134.340, 56.270, 52.070, 90.00, 95.24, 90.00
R / Rfree (%) n/a / n/a

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human VEGFR2 Kinase Domain with A Novel Pyrrolopyrimidine Inhibitor. (pdb code 3vhe). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Human VEGFR2 Kinase Domain with A Novel Pyrrolopyrimidine Inhibitor., PDB code: 3vhe:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 3vhe

Go back to Fluorine Binding Sites List in 3vhe
Fluorine binding site 1 out of 4 in the Crystal Structure of Human VEGFR2 Kinase Domain with A Novel Pyrrolopyrimidine 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 Human VEGFR2 Kinase Domain with A Novel Pyrrolopyrimidine Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1170

b:13.7
occ:1.00
F34 A:42Q1170 0.0 13.7 1.0
C22 A:42Q1170 1.3 12.2 1.0
C21 A:42Q1170 2.4 10.4 1.0
C23 A:42Q1170 2.4 11.2 1.0
N27 A:42Q1170 2.7 11.2 1.0
CG1 A:VAL916 3.5 10.0 1.0
CB A:LYS868 3.5 11.2 1.0
C20 A:42Q1170 3.7 11.2 1.0
C18 A:42Q1170 3.7 10.1 1.0
CD A:LYS868 3.7 13.8 1.0
CG2 A:VAL916 3.7 11.4 1.0
C28 A:42Q1170 3.8 11.1 1.0
C19 A:42Q1170 4.2 10.7 1.0
CG A:LYS868 4.2 13.2 1.0
CB A:VAL916 4.3 9.9 1.0
CG1 A:VAL914 4.4 13.1 1.0
OE2 A:GLU885 4.5 15.3 1.0
O31 A:42Q1170 4.5 11.7 1.0
O A:VAL914 4.6 10.1 1.0
N29 A:42Q1170 4.6 11.5 1.0
CG2 A:VAL899 4.7 21.1 1.0
N A:LYS868 4.7 9.8 1.0
CA A:LYS868 4.7 10.0 1.0
O17 A:42Q1170 4.9 10.7 1.0
CB A:VAL914 5.0 11.6 1.0
N4 A:42Q1170 5.0 11.7 1.0

Fluorine binding site 2 out of 4 in 3vhe

Go back to Fluorine Binding Sites List in 3vhe
Fluorine binding site 2 out of 4 in the Crystal Structure of Human VEGFR2 Kinase Domain with A Novel Pyrrolopyrimidine 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 Human VEGFR2 Kinase Domain with A Novel Pyrrolopyrimidine Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1170

b:23.5
occ:1.00
F45 A:42Q1170 0.0 23.5 1.0
C44 A:42Q1170 1.3 18.5 1.0
F47 A:42Q1170 2.2 21.6 1.0
F46 A:42Q1170 2.2 20.7 1.0
C38 A:42Q1170 2.3 16.4 1.0
C39 A:42Q1170 3.0 12.6 1.0
C37 A:42Q1170 3.4 16.5 1.0
CG1 A:VAL898 3.4 14.8 1.0
CG1 A:VAL899 4.0 20.1 1.0
O A:ILE1044 4.0 10.2 1.0
CD1 A:ILE892 4.3 12.4 1.0
C30 A:42Q1170 4.3 13.7 1.0
CD2 A:LEU889 4.5 14.5 1.0
C A:ILE1044 4.6 9.8 1.0
CD1 A:LEU1019 4.6 17.3 1.0
CA A:CYS1045 4.6 9.8 1.0
CG2 A:ILE1044 4.6 14.3 1.0
C36 A:42Q1170 4.6 15.3 1.0
CB A:VAL898 4.8 12.1 1.0
N A:CYS1045 4.9 9.5 1.0
N A:VAL899 4.9 11.0 1.0
CB A:ILE1044 5.0 10.4 1.0
O31 A:42Q1170 5.0 11.7 1.0

Fluorine binding site 3 out of 4 in 3vhe

Go back to Fluorine Binding Sites List in 3vhe
Fluorine binding site 3 out of 4 in the Crystal Structure of Human VEGFR2 Kinase Domain with A Novel Pyrrolopyrimidine 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 Human VEGFR2 Kinase Domain with A Novel Pyrrolopyrimidine Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1170

b:20.7
occ:1.00
F46 A:42Q1170 0.0 20.7 1.0
C44 A:42Q1170 1.3 18.5 1.0
F47 A:42Q1170 2.2 21.6 1.0
F45 A:42Q1170 2.2 23.5 1.0
C38 A:42Q1170 2.3 16.4 1.0
C39 A:42Q1170 2.9 12.6 1.0
C A:CYS1045 3.3 9.5 1.0
CA A:CYS1045 3.4 9.8 1.0
CG2 A:ILE1044 3.4 14.3 1.0
C37 A:42Q1170 3.5 16.5 1.0
O A:CYS1045 3.5 9.3 1.0
CD2 A:HIS1026 3.5 12.5 1.0
NE2 A:HIS1026 3.6 12.7 1.0
N A:CYS1045 3.6 9.5 1.0
C A:ILE1044 3.8 9.8 1.0
N A:ASP1046 3.8 10.3 1.0
O A:ILE1044 3.9 10.2 1.0
CB A:ASP1046 4.3 12.6 1.0
C30 A:42Q1170 4.3 13.7 1.0
CB A:ILE1044 4.3 10.4 1.0
O A:HOH2067 4.4 26.0 1.0
O31 A:42Q1170 4.6 11.7 1.0
CA A:ASP1046 4.6 10.4 1.0
C36 A:42Q1170 4.7 15.3 1.0
CE1 A:HIS1026 4.7 12.9 1.0
CG A:HIS1026 4.7 12.5 1.0
CA A:ILE1044 4.7 8.4 1.0
CB A:CYS1045 4.8 10.1 1.0
CG1 A:VAL899 4.9 20.1 1.0
C35 A:42Q1170 5.0 14.9 1.0

Fluorine binding site 4 out of 4 in 3vhe

Go back to Fluorine Binding Sites List in 3vhe
Fluorine binding site 4 out of 4 in the Crystal Structure of Human VEGFR2 Kinase Domain with A Novel Pyrrolopyrimidine Inhibitor.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Human VEGFR2 Kinase Domain with A Novel Pyrrolopyrimidine Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1170

b:21.6
occ:1.00
F47 A:42Q1170 0.0 21.6 1.0
C44 A:42Q1170 1.3 18.5 1.0
F45 A:42Q1170 2.2 23.5 1.0
F46 A:42Q1170 2.2 20.7 1.0
C38 A:42Q1170 2.3 16.4 1.0
C37 A:42Q1170 2.7 16.5 1.0
CD1 A:LEU1019 3.6 17.3 1.0
CD2 A:LEU1019 3.7 17.8 1.0
C39 A:42Q1170 3.7 12.6 1.0
O A:HOH2067 4.0 26.0 1.0
CD2 A:HIS1026 4.0 12.5 1.0
C36 A:42Q1170 4.1 15.3 1.0
CD1 A:ILE892 4.2 12.4 1.0
CG A:LEU1019 4.3 16.8 1.0
O A:HOH2109 4.4 29.8 1.0
NE2 A:HIS1026 4.6 12.7 1.0
CG2 A:ILE1044 4.6 14.3 1.0
CG A:HIS1026 4.7 12.5 1.0
C30 A:42Q1170 4.8 13.7 1.0

Reference:

Y.Oguro, N.Miyamoto, K.Okada, T.Takagi, H.Iwata, Y.Awazu, H.Miki, A.Hori, K.Kamiyama, S.Imamura. Design, Synthesis, and Evaluation of 5-Methyl-4-Phenoxy-5H-Pyrrolo[3,2-D]Pyrimidine Derivatives: Novel VEGFR2 Kinase Inhibitors Binding to Inactive Kinase Conformation. Bioorg.Med.Chem. V. 18 7260 2010.
ISSN: ISSN 0968-0896
PubMed: 20833055
DOI: 10.1016/J.BMC.2010.08.017
Page generated: Wed Jul 31 23:17:40 2024

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