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Fluorine in PDB 3r4p: 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: 3r4p 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) 19.99 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.245, 79.592, 118.648, 90.00, 90.00, 90.00
R / Rfree (%) 21.1 / 21.3

Other elements in 3r4p:

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 3r4p). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 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: 3r4p:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 3r4p

Go back to Fluorine Binding Sites List in 3r4p
Fluorine binding site 1 out of 4 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:17.4
occ:1.00
F1 A:FU7901 0.0 17.4 1.0
C20 A:FU7901 1.4 15.2 1.0
F2 A:FU7901 2.2 18.0 1.0
C21 A:FU7901 2.3 14.2 1.0
C19 A:FU7901 2.3 11.9 1.0
N5 A:FU7901 2.8 11.6 1.0
C13 A:FU7901 3.2 12.3 1.0
O1 A:FU7901 3.3 12.6 1.0
O A:HOH377 3.3 25.3 1.0
C18 A:FU7901 3.5 14.2 1.0
CE A:LYS58 3.6 25.4 1.0
CD A:LYS58 3.8 20.8 1.0
O A:HOH409 4.1 29.5 1.0
N1 A:FU7901 4.3 10.2 1.0
N7 A:FU7901 4.3 15.8 1.0
NZ A:LYS58 4.5 24.6 1.0
C17 A:FU7901 4.5 14.0 1.0
CG2 A:ILE96 4.8 10.9 1.0
ND2 A:ASN106 4.9 15.8 1.0

Fluorine binding site 2 out of 4 in 3r4p

Go back to Fluorine Binding Sites List in 3r4p
Fluorine binding site 2 out of 4 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:18.0
occ:1.00
F2 A:FU7901 0.0 18.0 1.0
C20 A:FU7901 1.4 15.2 1.0
F1 A:FU7901 2.2 17.4 1.0
C21 A:FU7901 2.3 14.2 1.0
C19 A:FU7901 2.3 11.9 1.0
N5 A:FU7901 2.8 11.6 1.0
CG2 A:ILE96 3.2 10.9 1.0
CD A:LYS58 3.4 20.8 1.0
CD1 A:ILE96 3.5 17.8 1.0
CG1 A:ILE96 3.8 12.7 1.0
CE A:LYS58 3.9 25.4 1.0
O A:HOH257 3.9 18.8 1.0
C13 A:FU7901 4.0 12.3 1.0
CB A:ILE96 4.0 10.7 1.0
O A:GLY97 4.3 10.4 1.0
NZ A:LYS58 4.5 24.6 1.0
O1 A:FU7901 4.5 12.6 1.0
C18 A:FU7901 4.6 14.2 1.0
CG A:LYS58 4.6 19.7 1.0
CB A:LYS58 4.7 14.7 1.0
N1 A:FU7901 4.8 10.2 1.0
O2 A:PO4903 4.9 25.8 1.0

Fluorine binding site 3 out of 4 in 3r4p

Go back to Fluorine Binding Sites List in 3r4p
Fluorine binding site 3 out of 4 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
B:F901

b:21.2
occ:1.00
F1 B:FU7901 0.0 21.2 1.0
C20 B:FU7901 1.4 17.4 1.0
F2 B:FU7901 2.2 21.8 1.0
C19 B:FU7901 2.3 13.4 1.0
C21 B:FU7901 2.3 17.3 1.0
N5 B:FU7901 2.8 10.3 1.0
O B:HOH239 3.0 34.5 1.0
O B:HOH359 3.4 45.2 1.0
C13 B:FU7901 3.4 9.3 1.0
C17 B:FU7901 3.5 13.1 1.0
CD B:LYS58 3.6 22.0 1.0
O1 B:FU7901 3.6 12.4 1.0
CE B:LYS58 4.0 25.3 1.0
O B:HOH381 4.2 31.1 1.0
C16 B:FU7901 4.5 10.8 1.0
N1 B:FU7901 4.5 7.5 1.0
C18 B:FU7901 4.5 11.4 1.0
CG2 B:ILE96 4.5 11.0 1.0

Fluorine binding site 4 out of 4 in 3r4p

Go back to Fluorine Binding Sites List in 3r4p
Fluorine binding site 4 out of 4 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:21.8
occ:1.00
F2 B:FU7901 0.0 21.8 1.0
C20 B:FU7901 1.3 17.4 1.0
F1 B:FU7901 2.2 21.2 1.0
C21 B:FU7901 2.3 17.3 1.0
C19 B:FU7901 2.3 13.4 1.0
N5 B:FU7901 2.8 10.3 1.0
CG2 B:ILE96 3.1 11.0 1.0
CD1 B:ILE96 3.3 16.2 1.0
CG1 B:ILE96 3.5 11.2 1.0
CB B:ILE96 3.9 9.0 1.0
O B:GLY97 3.9 9.9 1.0
C13 B:FU7901 4.1 9.3 1.0
CD B:LYS58 4.1 22.0 1.0
NE2 B:HIS154 4.6 11.0 1.0
CD2 B:HIS154 4.7 9.5 1.0
O1 B:FU7901 4.7 12.4 1.0
CB B:LYS58 4.9 12.6 1.0
OD2 B:ASP102 4.9 12.9 1.0
C17 B:FU7901 4.9 13.1 1.0
O B:HOH336 4.9 26.9 1.0
N1 B:FU7901 4.9 7.5 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 19:05:30 2025

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