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Fluorine in PDB 3r4n: Optimization of Potent, Selective, and Orally Bioavailable Pyrrolodinopyrimidine-Containing Inhibitors of Heat Shock Protein 90. Identification of Development Candidate 2-Amino-4-{4-Chloro-2-[2-(4- Fluoro-1H-Pyrazol-1-Yl)Ethoxy]-6-Methylphenyl}-N-(2,2- Difluoropropyl)-5,7-Dihydro-6H-Pyrrolo[3,4-D]Pyrimidine-6-Carboxamide

Protein crystallography data

The structure of Optimization of Potent, Selective, and Orally Bioavailable Pyrrolodinopyrimidine-Containing Inhibitors of Heat Shock Protein 90. Identification of Development Candidate 2-Amino-4-{4-Chloro-2-[2-(4- Fluoro-1H-Pyrazol-1-Yl)Ethoxy]-6-Methylphenyl}-N-(2,2- Difluoropropyl)-5,7-Dihydro-6H-Pyrrolo[3,4-D]Pyrimidine-6-Carboxamide, PDB code: 3r4n was solved by K.S.Gajiwala, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 17.74 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.875, 79.404, 118.506, 90.00, 90.00, 90.00
R / Rfree (%) 23.2 / 22

Other elements in 3r4n:

The structure of Optimization of Potent, Selective, and Orally Bioavailable Pyrrolodinopyrimidine-Containing Inhibitors of Heat Shock Protein 90. Identification of Development Candidate 2-Amino-4-{4-Chloro-2-[2-(4- Fluoro-1H-Pyrazol-1-Yl)Ethoxy]-6-Methylphenyl}-N-(2,2- Difluoropropyl)-5,7-Dihydro-6H-Pyrrolo[3,4-D]Pyrimidine-6-Carboxamide also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Optimization of Potent, Selective, and Orally Bioavailable Pyrrolodinopyrimidine-Containing Inhibitors of Heat Shock Protein 90. Identification of Development Candidate 2-Amino-4-{4-Chloro-2-[2-(4- Fluoro-1H-Pyrazol-1-Yl)Ethoxy]-6-Methylphenyl}-N-(2,2- Difluoropropyl)-5,7-Dihydro-6H-Pyrrolo[3,4-D]Pyrimidine-6-Carboxamide (pdb code 3r4n). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Optimization of Potent, Selective, and Orally Bioavailable Pyrrolodinopyrimidine-Containing Inhibitors of Heat Shock Protein 90. Identification of Development Candidate 2-Amino-4-{4-Chloro-2-[2-(4- Fluoro-1H-Pyrazol-1-Yl)Ethoxy]-6-Methylphenyl}-N-(2,2- Difluoropropyl)-5,7-Dihydro-6H-Pyrrolo[3,4-D]Pyrimidine-6-Carboxamide, PDB code: 3r4n:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3r4n

Go back to Fluorine Binding Sites List in 3r4n
Fluorine binding site 1 out of 6 in the Optimization of Potent, Selective, and Orally Bioavailable Pyrrolodinopyrimidine-Containing Inhibitors of Heat Shock Protein 90. Identification of Development Candidate 2-Amino-4-{4-Chloro-2-[2-(4- Fluoro-1H-Pyrazol-1-Yl)Ethoxy]-6-Methylphenyl}-N-(2,2- Difluoropropyl)-5,7-Dihydro-6H-Pyrrolo[3,4-D]Pyrimidine-6-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Optimization of Potent, Selective, and Orally Bioavailable Pyrrolodinopyrimidine-Containing Inhibitors of Heat Shock Protein 90. Identification of Development Candidate 2-Amino-4-{4-Chloro-2-[2-(4- Fluoro-1H-Pyrazol-1-Yl)Ethoxy]-6-Methylphenyl}-N-(2,2- Difluoropropyl)-5,7-Dihydro-6H-Pyrrolo[3,4-D]Pyrimidine-6-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:38.0
occ:1.00
 F21 A:FU5901 0.0 38.0 1.0
C20 A:FU5901 1.4 33.6 1.0
F23 A:FU5901 2.2 33.2 1.0
F22 A:FU5901 2.2 35.0 1.0
C19 A:FU5901 2.4 31.6 1.0
C18 A:FU5901 2.9 29.0 1.0
O A:HOH385 4.1 29.5 1.0
C14 A:FU5901 4.3 27.4 1.0
CB A:ASP54 4.4 15.6 1.0
CD A:LYS58 4.5 32.9 1.0
O A:ASP54 4.7 15.0 1.0
C A:ASP54 4.8 13.8 1.0
O A:HOH277 4.9 36.8 1.0
N A:ALA55 4.9 11.9 1.0

Fluorine binding site 2 out of 6 in 3r4n

Go back to Fluorine Binding Sites List in 3r4n
Fluorine binding site 2 out of 6 in the Optimization of Potent, Selective, and Orally Bioavailable Pyrrolodinopyrimidine-Containing Inhibitors of Heat Shock Protein 90. Identification of Development Candidate 2-Amino-4-{4-Chloro-2-[2-(4- Fluoro-1H-Pyrazol-1-Yl)Ethoxy]-6-Methylphenyl}-N-(2,2- Difluoropropyl)-5,7-Dihydro-6H-Pyrrolo[3,4-D]Pyrimidine-6-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Optimization of Potent, Selective, and Orally Bioavailable Pyrrolodinopyrimidine-Containing Inhibitors of Heat Shock Protein 90. Identification of Development Candidate 2-Amino-4-{4-Chloro-2-[2-(4- Fluoro-1H-Pyrazol-1-Yl)Ethoxy]-6-Methylphenyl}-N-(2,2- Difluoropropyl)-5,7-Dihydro-6H-Pyrrolo[3,4-D]Pyrimidine-6-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:35.0
occ:1.00
 F22 A:FU5901 0.0 35.0 1.0
C20 A:FU5901 1.4 33.6 1.0
F23 A:FU5901 2.2 33.2 1.0
F21 A:FU5901 2.2 38.0 1.0
C19 A:FU5901 2.4 31.6 1.0
O A:HOH277 3.5 36.8 1.0
CD A:LYS58 3.7 32.9 1.0
C18 A:FU5901 3.8 29.0 1.0
CG2 A:ILE96 3.9 14.0 1.0
C16 A:FU5901 4.0 15.3 1.0
CA A:ALA55 4.2 12.1 1.0
CB A:ALA55 4.5 11.3 1.0
CB A:LYS58 4.6 21.4 1.0
C11 A:FU5901 4.6 14.2 1.0
CE A:LYS58 4.6 36.4 1.0
N A:ALA55 4.6 11.9 1.0
CG A:LYS58 4.8 28.2 1.0
O A:HOH282 4.8 17.2 1.0
C5 A:FU5901 4.9 13.3 1.0
O A:ASP54 4.9 15.0 1.0
C14 A:FU5901 4.9 27.4 1.0
C A:ASP54 4.9 13.8 1.0

Fluorine binding site 3 out of 6 in 3r4n

Go back to Fluorine Binding Sites List in 3r4n
Fluorine binding site 3 out of 6 in the Optimization of Potent, Selective, and Orally Bioavailable Pyrrolodinopyrimidine-Containing Inhibitors of Heat Shock Protein 90. Identification of Development Candidate 2-Amino-4-{4-Chloro-2-[2-(4- Fluoro-1H-Pyrazol-1-Yl)Ethoxy]-6-Methylphenyl}-N-(2,2- Difluoropropyl)-5,7-Dihydro-6H-Pyrrolo[3,4-D]Pyrimidine-6-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Optimization of Potent, Selective, and Orally Bioavailable Pyrrolodinopyrimidine-Containing Inhibitors of Heat Shock Protein 90. Identification of Development Candidate 2-Amino-4-{4-Chloro-2-[2-(4- Fluoro-1H-Pyrazol-1-Yl)Ethoxy]-6-Methylphenyl}-N-(2,2- Difluoropropyl)-5,7-Dihydro-6H-Pyrrolo[3,4-D]Pyrimidine-6-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:33.2
occ:1.00
 F23 A:FU5901 0.0 33.2 1.0
C20 A:FU5901 1.4 33.6 1.0
F22 A:FU5901 2.2 35.0 1.0
F21 A:FU5901 2.2 38.0 1.0
C19 A:FU5901 2.4 31.6 1.0
N A:ALA55 3.0 11.9 1.0
C18 A:FU5901 3.0 29.0 1.0
CA A:ALA55 3.2 12.1 1.0
C A:ASP54 3.2 13.8 1.0
CB A:ASP54 3.3 15.6 1.0
O A:ASP54 3.6 15.0 1.0
CB A:ALA55 3.7 11.3 1.0
O A:ASN51 3.8 12.5 1.0
CA A:ASP54 3.9 14.7 1.0
C14 A:FU5901 4.4 27.4 1.0
O A:HOH385 4.5 29.5 1.0
O8 A:FU5901 4.6 23.1 1.0
C A:ALA55 4.6 12.6 1.0
CG A:ASP54 4.7 18.6 1.0
C11 A:FU5901 4.7 14.2 1.0
C16 A:FU5901 4.7 15.3 1.0
N A:ASP54 4.8 14.3 1.0
C A:ASN51 4.9 12.5 1.0
OD2 A:ASP54 5.0 18.0 1.0
C5 A:FU5901 5.0 13.3 1.0

Fluorine binding site 4 out of 6 in 3r4n

Go back to Fluorine Binding Sites List in 3r4n
Fluorine binding site 4 out of 6 in the Optimization of Potent, Selective, and Orally Bioavailable Pyrrolodinopyrimidine-Containing Inhibitors of Heat Shock Protein 90. Identification of Development Candidate 2-Amino-4-{4-Chloro-2-[2-(4- Fluoro-1H-Pyrazol-1-Yl)Ethoxy]-6-Methylphenyl}-N-(2,2- Difluoropropyl)-5,7-Dihydro-6H-Pyrrolo[3,4-D]Pyrimidine-6-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Optimization of Potent, Selective, and Orally Bioavailable Pyrrolodinopyrimidine-Containing Inhibitors of Heat Shock Protein 90. Identification of Development Candidate 2-Amino-4-{4-Chloro-2-[2-(4- Fluoro-1H-Pyrazol-1-Yl)Ethoxy]-6-Methylphenyl}-N-(2,2- Difluoropropyl)-5,7-Dihydro-6H-Pyrrolo[3,4-D]Pyrimidine-6-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F901

b:36.4
occ:1.00
 F21 B:FU5901 0.0 36.4 1.0
C20 B:FU5901 1.4 33.5 1.0
F22 B:FU5901 2.2 34.4 1.0
F23 B:FU5901 2.2 33.5 1.0
C19 B:FU5901 2.4 31.7 1.0
C18 B:FU5901 3.0 29.3 1.0
CD B:LYS58 3.4 30.4 1.0
CE B:LYS58 3.5 33.5 1.0
CG B:LYS58 3.9 25.3 1.0
CB B:ASP54 4.3 15.2 1.0
C14 B:FU5901 4.4 28.6 1.0
O B:ASP54 4.6 14.7 1.0
C B:ASP54 4.7 14.5 1.0
NZ B:LYS58 4.8 35.9 1.0
O B:HOH311 4.8 26.0 1.0

Fluorine binding site 5 out of 6 in 3r4n

Go back to Fluorine Binding Sites List in 3r4n
Fluorine binding site 5 out of 6 in the Optimization of Potent, Selective, and Orally Bioavailable Pyrrolodinopyrimidine-Containing Inhibitors of Heat Shock Protein 90. Identification of Development Candidate 2-Amino-4-{4-Chloro-2-[2-(4- Fluoro-1H-Pyrazol-1-Yl)Ethoxy]-6-Methylphenyl}-N-(2,2- Difluoropropyl)-5,7-Dihydro-6H-Pyrrolo[3,4-D]Pyrimidine-6-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Optimization of Potent, Selective, and Orally Bioavailable Pyrrolodinopyrimidine-Containing Inhibitors of Heat Shock Protein 90. Identification of Development Candidate 2-Amino-4-{4-Chloro-2-[2-(4- Fluoro-1H-Pyrazol-1-Yl)Ethoxy]-6-Methylphenyl}-N-(2,2- Difluoropropyl)-5,7-Dihydro-6H-Pyrrolo[3,4-D]Pyrimidine-6-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F901

b:34.4
occ:1.00
 F22 B:FU5901 0.0 34.4 1.0
C20 B:FU5901 1.4 33.5 1.0
F23 B:FU5901 2.2 33.5 1.0
F21 B:FU5901 2.2 36.4 1.0
C19 B:FU5901 2.4 31.7 1.0
CD B:LYS58 3.2 30.4 1.0
O B:HOH311 3.4 26.0 1.0
C18 B:FU5901 3.8 29.3 1.0
CG B:LYS58 3.8 25.3 1.0
CG2 B:ILE96 3.9 13.2 1.0
C16 B:FU5901 4.0 13.4 1.0
CE B:LYS58 4.1 33.5 1.0
CA B:ALA55 4.2 12.7 1.0
CB B:LYS58 4.6 18.8 1.0
O B:HOH291 4.6 20.7 1.0
CB B:ALA55 4.6 10.5 1.0
N B:ALA55 4.6 13.5 1.0
C11 B:FU5901 4.6 16.4 1.0
O B:ASP54 4.7 14.7 1.0
C B:ASP54 4.8 14.5 1.0
C5 B:FU5901 4.8 15.8 1.0
C14 B:FU5901 4.9 28.6 1.0

Fluorine binding site 6 out of 6 in 3r4n

Go back to Fluorine Binding Sites List in 3r4n
Fluorine binding site 6 out of 6 in the Optimization of Potent, Selective, and Orally Bioavailable Pyrrolodinopyrimidine-Containing Inhibitors of Heat Shock Protein 90. Identification of Development Candidate 2-Amino-4-{4-Chloro-2-[2-(4- Fluoro-1H-Pyrazol-1-Yl)Ethoxy]-6-Methylphenyl}-N-(2,2- Difluoropropyl)-5,7-Dihydro-6H-Pyrrolo[3,4-D]Pyrimidine-6-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Optimization of Potent, Selective, and Orally Bioavailable Pyrrolodinopyrimidine-Containing Inhibitors of Heat Shock Protein 90. Identification of Development Candidate 2-Amino-4-{4-Chloro-2-[2-(4- Fluoro-1H-Pyrazol-1-Yl)Ethoxy]-6-Methylphenyl}-N-(2,2- Difluoropropyl)-5,7-Dihydro-6H-Pyrrolo[3,4-D]Pyrimidine-6-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F901

b:33.5
occ:1.00
 F23 B:FU5901 0.0 33.5 1.0
C20 B:FU5901 1.4 33.5 1.0
F22 B:FU5901 2.2 34.4 1.0
F21 B:FU5901 2.2 36.4 1.0
C19 B:FU5901 2.4 31.7 1.0
N B:ALA55 3.0 13.5 1.0
C18 B:FU5901 3.0 29.3 1.0
C B:ASP54 3.1 14.5 1.0
CB B:ASP54 3.2 15.2 1.0
CA B:ALA55 3.3 12.7 1.0
O B:ASP54 3.4 14.7 1.0
CA B:ASP54 3.8 13.8 1.0
CB B:ALA55 3.8 10.5 1.0
O B:ASN51 3.8 12.3 1.0
CG B:LYS58 4.1 25.3 1.0
CD B:LYS58 4.3 30.4 1.0
C14 B:FU5901 4.4 28.6 1.0
CG B:ASP54 4.5 14.8 1.0
O8 B:FU5901 4.6 25.7 1.0
C B:ALA55 4.6 11.9 1.0
N B:ASP54 4.7 13.0 1.0
C16 B:FU5901 4.8 13.4 1.0
C11 B:FU5901 4.8 16.4 1.0
OD2 B:ASP54 4.8 17.2 1.0
C B:ASN51 4.9 14.3 1.0
CE B:LYS58 5.0 33.5 1.0

Reference:

L.Zehnder, M.Bennett, J.Meng, B.Huang, S.Ninkovic, F.Wang, J.Braganza, J.Tatlock, T.Jewell, J.Z.Zhou, B.Burke, J.Wang, K.Maegley, P.P.Mehta, M.J.Yin, K.S.Gajiwala, M.J.Hickey, S.Yamazaki, E.Smith, P.Kang, A.Sistla, E.Dovalsantos, M.R.Gehring, R.Kania, M.Wythes, P.P.Kung. Optimization of Potent, Selective, and Orally Bioavailable Pyrrolodinopyrimidine-Containing Inhibitors of Heat Shock Protein 90. Identification of Development Candidate 2-Amino-4-{4-Chloro-2-[2-(4-Fluoro-1H-Pyrazol-1-Yl)Ethoxy]- 6-Methylphenyl}-N-(2,2-Difluoropropyl)-5,7-Dihydro-6H- Pyrrolo[3,4-D]Pyrimidine-6-Carboxamide. J.Med.Chem. V. 54 3368 2011.
ISSN: ISSN 0022-2623
PubMed: 21438541
DOI: 10.1021/JM200128M
Page generated: Mon Jul 14 19:04:13 2025

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