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Fluorine in PDB 3r4o: 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: 3r4o 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) 19.88 / 2.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 43.149, 79.523, 130.101, 90.00, 90.00, 90.00
R / Rfree (%) 23.5 / 30.8

Other elements in 3r4o:

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) 4 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 3r4o). 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: 3r4o:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3r4o

Go back to Fluorine Binding Sites List in 3r4o
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:26.6
occ:1.00
F29 A:FU3901 0.0 26.6 1.0
C21 A:FU3901 1.3 24.7 1.0
F30 A:FU3901 2.2 25.7 1.0
F31 A:FU3901 2.2 23.4 1.0
C9 A:FU3901 2.3 25.1 1.0
C8 A:FU3901 2.9 22.3 1.0
CB A:ASP54 3.6 17.1 1.0
NZ A:LYS58 3.6 23.8 1.0
O A:ASP54 4.1 14.1 1.0
C A:ASP54 4.1 13.8 1.0
CE A:LYS58 4.1 25.9 1.0
C10 A:FU3901 4.3 22.3 1.0
CD A:LYS58 4.4 24.8 1.0
OD2 A:ASP54 4.5 23.4 1.0
CA A:ASP54 4.5 16.1 1.0
N A:ALA55 4.5 11.7 1.0
CG A:ASP54 4.5 20.0 1.0
CA A:ALA55 4.9 11.2 1.0
O28 A:FU3901 4.9 23.3 1.0

Fluorine binding site 2 out of 6 in 3r4o

Go back to Fluorine Binding Sites List in 3r4o
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:25.7
occ:1.00
F30 A:FU3901 0.0 25.7 1.0
C21 A:FU3901 1.3 24.7 1.0
F31 A:FU3901 2.2 23.4 1.0
F29 A:FU3901 2.2 26.6 1.0
C9 A:FU3901 2.3 25.1 1.0
C20 A:FU3901 3.7 20.6 1.0
N26 A:FU3901 3.7 20.9 1.0
C8 A:FU3901 3.7 22.3 1.0
N25 A:FU3901 3.9 21.8 1.0
CD A:LYS58 3.9 24.8 1.0
C7 A:FU3901 3.9 20.1 1.0
O27 A:FU3901 4.1 20.8 1.0
C4 A:FU3901 4.1 22.3 1.0
NZ A:LYS58 4.2 23.8 1.0
C6 A:FU3901 4.2 20.4 1.0
CG2 A:ILE96 4.3 14.7 1.0
CE A:LYS58 4.4 25.9 1.0
CA A:ALA55 4.5 11.2 1.0
C15 A:FU3901 4.6 18.9 1.0
C19 A:FU3901 4.6 21.4 1.0
CB A:LYS58 4.7 18.6 1.0
C14 A:FU3901 4.7 20.4 1.0
O A:ASP54 4.7 14.1 1.0
N A:ALA55 4.7 11.7 1.0
CG A:LYS58 4.7 21.8 1.0
C10 A:FU3901 4.8 22.3 1.0
C A:ASP54 4.8 13.8 1.0
O28 A:FU3901 4.9 23.3 1.0
CB A:ALA55 4.9 9.1 1.0

Fluorine binding site 3 out of 6 in 3r4o

Go back to Fluorine Binding Sites List in 3r4o
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:23.4
occ:1.00
F31 A:FU3901 0.0 23.4 1.0
C21 A:FU3901 1.3 24.7 1.0
F30 A:FU3901 2.2 25.7 1.0
F29 A:FU3901 2.2 26.6 1.0
C9 A:FU3901 2.4 25.1 1.0
C8 A:FU3901 2.9 22.3 1.0
N A:ALA55 3.0 11.7 1.0
CA A:ALA55 3.3 11.2 1.0
C A:ASP54 3.3 13.8 1.0
CB A:ASP54 3.4 17.1 1.0
O A:ASN51 3.6 14.2 1.0
CB A:ALA55 3.7 9.1 1.0
O A:ASP54 3.7 14.1 1.0
CA A:ASP54 4.0 16.1 1.0
C15 A:FU3901 4.1 18.9 1.0
C7 A:FU3901 4.2 20.1 1.0
O28 A:FU3901 4.2 23.3 1.0
C10 A:FU3901 4.2 22.3 1.0
C14 A:FU3901 4.4 20.4 1.0
N26 A:FU3901 4.4 20.9 1.0
N23 A:FU3901 4.5 19.1 1.0
C6 A:FU3901 4.6 20.4 1.0
C A:ASN51 4.7 14.6 1.0
C A:ALA55 4.7 10.6 1.0
N A:ASP54 4.7 17.4 1.0
CG A:ASP54 4.8 20.0 1.0
CG2 A:ILE96 4.9 14.7 1.0
C17 A:FU3901 5.0 21.0 1.0

Fluorine binding site 4 out of 6 in 3r4o

Go back to Fluorine Binding Sites List in 3r4o
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:30.7
occ:1.00
F29 B:FU3901 0.0 30.7 1.0
C21 B:FU3901 1.3 27.0 1.0
F30 B:FU3901 2.2 29.7 1.0
F31 B:FU3901 2.2 29.3 1.0
C9 B:FU3901 2.3 25.8 1.0
C8 B:FU3901 2.9 23.2 1.0
CD B:LYS58 3.5 12.3 1.0
NZ B:LYS58 4.0 16.2 1.0
CE B:LYS58 4.1 16.2 1.0
CG B:LYS58 4.2 11.5 1.0
CB B:ASP54 4.2 11.3 1.0
C10 B:FU3901 4.3 23.6 1.0
O B:ASP54 4.6 10.2 1.0
C B:ASP54 4.6 9.2 1.0
N B:ALA55 4.9 8.3 1.0
O28 B:FU3901 4.9 22.7 1.0

Fluorine binding site 5 out of 6 in 3r4o

Go back to Fluorine Binding Sites List in 3r4o
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:29.7
occ:1.00
F30 B:FU3901 0.0 29.7 1.0
C21 B:FU3901 1.3 27.0 1.0
F29 B:FU3901 2.2 30.7 1.0
F31 B:FU3901 2.2 29.3 1.0
C9 B:FU3901 2.3 25.8 1.0
CD B:LYS58 3.0 12.3 1.0
N26 B:FU3901 3.6 21.6 1.0
C7 B:FU3901 3.7 20.4 1.0
C8 B:FU3901 3.7 23.2 1.0
C20 B:FU3901 3.7 23.2 1.0
N25 B:FU3901 3.9 23.6 1.0
CA B:ALA55 4.0 8.2 1.0
CG B:LYS58 4.0 11.5 1.0
CE B:LYS58 4.1 16.2 1.0
C6 B:FU3901 4.2 20.6 1.0
CB B:ALA55 4.2 6.2 1.0
CG2 B:ILE96 4.2 10.5 1.0
O27 B:FU3901 4.3 25.1 1.0
C15 B:FU3901 4.3 21.0 1.0
N B:ALA55 4.3 8.3 1.0
C4 B:FU3901 4.3 22.1 1.0
C14 B:FU3901 4.5 20.8 1.0
C B:ASP54 4.6 9.2 1.0
O B:ASP54 4.6 10.2 1.0
NZ B:LYS58 4.7 16.2 1.0
C19 B:FU3901 4.7 22.0 1.0
O28 B:FU3901 4.8 22.7 1.0
C10 B:FU3901 4.8 23.6 1.0
CB B:LYS58 4.9 9.5 1.0

Fluorine binding site 6 out of 6 in 3r4o

Go back to Fluorine Binding Sites List in 3r4o
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:29.3
occ:1.00
F31 B:FU3901 0.0 29.3 1.0
C21 B:FU3901 1.3 27.0 1.0
F30 B:FU3901 2.2 29.7 1.0
F29 B:FU3901 2.2 30.7 1.0
C9 B:FU3901 2.3 25.8 1.0
C8 B:FU3901 2.9 23.2 1.0
N B:ALA55 3.0 8.3 1.0
CB B:ASP54 3.0 11.3 1.0
C B:ASP54 3.2 9.2 1.0
CA B:ALA55 3.4 8.2 1.0
O B:ASN51 3.6 11.6 1.0
O B:ASP54 3.6 10.2 1.0
CA B:ASP54 3.7 9.7 1.0
CB B:ALA55 3.8 6.2 1.0
CD B:LYS58 4.2 12.3 1.0
C10 B:FU3901 4.3 23.6 1.0
CG B:ASP54 4.4 12.2 1.0
O28 B:FU3901 4.4 22.7 1.0
CG B:LYS58 4.6 11.5 1.0
N B:ASP54 4.6 7.9 1.0
OD2 B:ASP54 4.6 14.7 1.0
C B:ASN51 4.6 10.5 1.0
C15 B:FU3901 4.7 21.0 1.0
C7 B:FU3901 4.8 20.4 1.0
C B:ALA55 4.9 7.9 1.0
C14 B:FU3901 4.9 20.8 1.0
CA B:ASN51 5.0 10.7 1.0
N26 B:FU3901 5.0 21.6 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: Sun Dec 13 11:54:15 2020

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