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Fluorine in PDB 3rcd: HER2 Kinase Domain Complexed with Tak-285

Enzymatic activity of HER2 Kinase Domain Complexed with Tak-285

All present enzymatic activity of HER2 Kinase Domain Complexed with Tak-285:
2.7.10.1;

Protein crystallography data

The structure of HER2 Kinase Domain Complexed with Tak-285, PDB code: 3rcd was solved by K.Aertgeerts, R.Skene, S.Sogabe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 3.21
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 50.542, 64.936, 92.360, 90.42, 89.72, 90.35
R / Rfree (%) 22.4 / 29.4

Other elements in 3rcd:

The structure of HER2 Kinase Domain Complexed with Tak-285 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the HER2 Kinase Domain Complexed with Tak-285 (pdb code 3rcd). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the HER2 Kinase Domain Complexed with Tak-285, PDB code: 3rcd:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3rcd

Go back to Fluorine Binding Sites List in 3rcd
Fluorine binding site 1 out of 6 in the HER2 Kinase Domain Complexed with Tak-285


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of HER2 Kinase Domain Complexed with Tak-285 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F9001

b:34.3
occ:1.00
 F2 A:03P9001 0.0 34.3 1.0
C22 A:03P9001 1.4 33.5 1.0
F A:03P9001 2.2 34.6 1.0
F1 A:03P9001 2.2 32.9 1.0
C20 A:03P9001 2.4 33.2 1.0
C21 A:03P9001 2.9 32.3 1.0
CD1 A:LEU785 3.1 29.2 1.0
OG1 A:THR798 3.2 32.4 1.0
N A:LEU785 3.3 29.9 1.0
CA A:LEU785 3.4 29.3 1.0
C19 A:03P9001 3.5 33.4 1.0
CB A:LEU785 3.6 29.8 1.0
C A:ARG784 3.7 30.4 1.0
CB A:THR798 3.7 31.9 1.0
O A:SER783 3.8 30.4 1.0
CG A:LEU785 4.0 29.9 1.0
OG A:SER783 4.0 28.5 1.0
O A:ARG784 4.1 30.2 1.0
C A:SER783 4.1 29.9 1.0
C16 A:03P9001 4.2 32.1 1.0
N A:ARG784 4.3 30.2 1.0
CA A:ARG784 4.4 31.1 1.0
CG2 A:THR798 4.4 31.3 1.0
OG1 A:THR862 4.5 37.8 1.0
CB A:SER783 4.6 28.6 1.0
C18 A:03P9001 4.6 33.6 1.0
C A:LEU785 4.9 29.4 1.0
C17 A:03P9001 4.9 32.9 1.0
CA A:SER783 5.0 29.4 1.0

Fluorine binding site 2 out of 6 in 3rcd

Go back to Fluorine Binding Sites List in 3rcd
Fluorine binding site 2 out of 6 in the HER2 Kinase Domain Complexed with Tak-285


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of HER2 Kinase Domain Complexed with Tak-285 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F9001

b:34.6
occ:1.00
 F A:03P9001 0.0 34.6 1.0
C22 A:03P9001 1.4 33.5 1.0
F2 A:03P9001 2.2 34.3 1.0
F1 A:03P9001 2.2 32.9 1.0
C20 A:03P9001 2.4 33.2 1.0
C19 A:03P9001 2.7 33.4 1.0
O A:SER783 3.1 30.4 1.0
CZ A:PHE864 3.3 43.5 1.0
C21 A:03P9001 3.6 32.3 1.0
CE2 A:PHE864 3.7 44.3 1.0
C A:SER783 4.0 29.9 1.0
N A:LEU785 4.0 29.9 1.0
C18 A:03P9001 4.0 33.6 1.0
CB A:LEU785 4.2 29.8 1.0
CD1 A:LEU785 4.2 29.2 1.0
CE1 A:PHE864 4.3 43.0 1.0
C A:ARG784 4.5 30.4 1.0
CA A:LEU785 4.5 29.3 1.0
CG A:MET774 4.5 84.8 1.0
OG1 A:THR862 4.6 37.8 1.0
N A:ARG784 4.6 30.2 1.0
CA A:ARG784 4.6 31.1 1.0
CB A:SER783 4.7 28.6 1.0
C16 A:03P9001 4.7 32.1 1.0
OG A:SER783 4.8 28.5 1.0
CG A:LEU785 4.8 29.9 1.0
CD2 A:PHE864 4.9 44.4 1.0
C17 A:03P9001 4.9 32.9 1.0
CA A:SER783 4.9 29.4 1.0

Fluorine binding site 3 out of 6 in 3rcd

Go back to Fluorine Binding Sites List in 3rcd
Fluorine binding site 3 out of 6 in the HER2 Kinase Domain Complexed with Tak-285


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of HER2 Kinase Domain Complexed with Tak-285 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F9001

b:32.9
occ:1.00
 F1 A:03P9001 0.0 32.9 1.0
C22 A:03P9001 1.4 33.5 1.0
F A:03P9001 2.2 34.6 1.0
F2 A:03P9001 2.2 34.3 1.0
C20 A:03P9001 2.3 33.2 1.0
OG1 A:THR862 2.7 37.8 1.0
OG A:SER783 2.9 28.5 1.0
CB A:SER783 2.9 28.6 1.0
C21 A:03P9001 3.0 32.3 1.0
O A:SER783 3.0 30.4 1.0
C19 A:03P9001 3.3 33.4 1.0
C A:SER783 3.4 29.9 1.0
CA A:SER783 3.7 29.4 1.0
CB A:THR862 3.8 37.5 1.0
CA A:THR862 4.1 37.9 1.0
CZ A:PHE864 4.2 43.5 1.0
N A:ARG784 4.2 30.2 1.0
C16 A:03P9001 4.3 32.1 1.0
N A:ASP863 4.3 39.7 1.0
OG1 A:THR798 4.4 32.4 1.0
C18 A:03P9001 4.5 33.6 1.0
CE1 A:PHE864 4.5 43.0 1.0
N A:SER783 4.6 29.7 1.0
O A:ILE861 4.7 37.3 1.0
C A:THR862 4.7 38.6 1.0
C A:ARG784 4.8 30.4 1.0
N A:LEU785 4.8 29.9 1.0
CA A:ARG784 4.8 31.1 1.0
C17 A:03P9001 4.9 32.9 1.0
CE2 A:PHE864 5.0 44.3 1.0
CB A:THR798 5.0 31.9 1.0

Fluorine binding site 4 out of 6 in 3rcd

Go back to Fluorine Binding Sites List in 3rcd
Fluorine binding site 4 out of 6 in the HER2 Kinase Domain Complexed with Tak-285


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of HER2 Kinase Domain Complexed with Tak-285 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F9001

b:47.4
occ:1.00
 F2 C:03P9001 0.0 47.4 1.0
C22 C:03P9001 1.4 47.0 1.0
F C:03P9001 2.2 47.3 1.0
F1 C:03P9001 2.2 46.3 1.0
C20 C:03P9001 2.4 46.9 1.0
CD1 C:LEU785 3.1 29.7 1.0
N C:LEU785 3.1 30.9 1.0
C21 C:03P9001 3.2 46.2 1.0
C19 C:03P9001 3.2 47.7 1.0
CA C:LEU785 3.3 30.4 1.0
OG1 C:THR798 3.3 33.2 1.0
CB C:LEU785 3.4 30.7 1.0
C C:ARG784 3.5 31.5 1.0
O C:SER783 3.7 30.9 1.0
CG C:LEU785 3.9 30.7 1.0
CB C:THR798 3.9 32.6 1.0
O C:ARG784 4.0 31.5 1.0
C C:SER783 4.1 30.6 1.0
OG C:SER783 4.1 28.8 1.0
CA C:ARG784 4.2 32.4 1.0
N C:ARG784 4.2 31.2 1.0
C16 C:03P9001 4.4 46.5 1.0
C18 C:03P9001 4.4 47.7 1.0
CB C:SER783 4.6 28.8 1.0
CG2 C:THR798 4.6 31.9 1.0
OG1 C:THR862 4.7 37.9 1.0
C C:LEU785 4.8 30.9 1.0
C17 C:03P9001 4.9 47.2 1.0
CD2 C:LEU785 4.9 31.8 1.0

Fluorine binding site 5 out of 6 in 3rcd

Go back to Fluorine Binding Sites List in 3rcd
Fluorine binding site 5 out of 6 in the HER2 Kinase Domain Complexed with Tak-285


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of HER2 Kinase Domain Complexed with Tak-285 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F9001

b:47.3
occ:1.00
 F C:03P9001 0.0 47.3 1.0
C22 C:03P9001 1.4 47.0 1.0
F2 C:03P9001 2.2 47.4 1.0
F1 C:03P9001 2.2 46.3 1.0
C20 C:03P9001 2.4 46.9 1.0
O C:SER783 2.7 30.9 1.0
C19 C:03P9001 2.8 47.7 1.0
CZ C:PHE864 3.1 43.8 1.0
C C:SER783 3.5 30.6 1.0
C21 C:03P9001 3.6 46.2 1.0
CE2 C:PHE864 3.8 44.5 1.0
CE1 C:PHE864 3.9 43.1 1.0
CB C:SER783 4.0 28.8 1.0
OG1 C:THR862 4.0 37.9 1.0
C18 C:03P9001 4.1 47.7 1.0
OG C:SER783 4.1 28.8 1.0
N C:LEU785 4.3 30.9 1.0
N C:ARG784 4.3 31.2 1.0
CA C:SER783 4.3 29.8 1.0
CA C:ARG784 4.6 32.4 1.0
C C:ARG784 4.6 31.5 1.0
C16 C:03P9001 4.7 46.5 1.0
N C:ASP863 4.7 39.6 1.0
CA C:THR862 4.9 37.6 1.0
CB C:LEU785 4.9 30.7 1.0
CD1 C:LEU785 4.9 29.7 1.0
CD2 C:PHE864 4.9 44.5 1.0
C17 C:03P9001 4.9 47.2 1.0
CA C:LEU785 5.0 30.4 1.0
N C:SER783 5.0 30.0 1.0
CB C:THR862 5.0 37.3 1.0

Fluorine binding site 6 out of 6 in 3rcd

Go back to Fluorine Binding Sites List in 3rcd
Fluorine binding site 6 out of 6 in the HER2 Kinase Domain Complexed with Tak-285


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of HER2 Kinase Domain Complexed with Tak-285 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F9001

b:46.3
occ:1.00
 F1 C:03P9001 0.0 46.3 1.0
C22 C:03P9001 1.4 47.0 1.0
F2 C:03P9001 2.2 47.4 1.0
F C:03P9001 2.2 47.3 1.0
C20 C:03P9001 2.3 46.9 1.0
OG C:SER783 2.5 28.8 1.0
OG1 C:THR862 2.6 37.9 1.0
C21 C:03P9001 2.7 46.2 1.0
CB C:SER783 3.0 28.8 1.0
C19 C:03P9001 3.5 47.7 1.0
O C:SER783 3.6 30.9 1.0
C C:SER783 3.7 30.6 1.0
OG1 C:THR798 3.8 33.2 1.0
CB C:THR862 3.8 37.3 1.0
CA C:SER783 4.0 29.8 1.0
C16 C:03P9001 4.1 46.5 1.0
CG2 C:THR798 4.3 31.9 1.0
N C:ARG784 4.3 31.2 1.0
CB C:THR798 4.3 32.6 1.0
CA C:THR862 4.4 37.6 1.0
N C:ASP863 4.6 39.6 1.0
C18 C:03P9001 4.7 47.7 1.0
C C:ARG784 4.8 31.5 1.0
C17 C:03P9001 4.9 47.2 1.0
N C:LEU785 4.9 30.9 1.0
C13 C:03P9001 4.9 46.9 1.0
CZ C:PHE864 4.9 43.8 1.0
O1 C:03P9001 5.0 46.9 1.0
N C:SER783 5.0 30.0 1.0
CA C:ARG784 5.0 32.4 1.0

Reference:

T.Ishikawa, M.Seto, H.Banno, Y.Kawakita, M.Oorui, T.Taniguchi, Y.Ohta, T.Tamura, A.Nakayama, H.Miki, H.Kamiguchi, T.Tanaka, N.Habuka, S.Sogabe, J.Yano, K.Aertgeerts, K.Kamiyama. Design and Synthesis of Novel Human Epidermal Growth Factor Receptor 2 (HER2)/Epidermal Growth Factor Receptor (Egfr) Dual Inhibitors Bearing A Pyrrolo[3,2-D]Pyrimidine Scaffold. J.Med.Chem. V. 54 8030 2011.
ISSN: ISSN 0022-2623
PubMed: 22003817
DOI: 10.1021/JM2008634
Page generated: Wed Jul 31 22:15:54 2024

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