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Fluorine in PDB 4x7o: Co-Crystal Structure of Perk Bound to 1-[5-(4-Amino-2,7-Dimethyl-7H- Pyrrolo[2,3-D]Pyrimidin-5-Yl)-2,3-Dihydro-1H-Indol-1-Yl]-2-[3-Fluoro- 5-(Trifluoromethyl)Phenyl]Ethanone Inhibitor

Enzymatic activity of Co-Crystal Structure of Perk Bound to 1-[5-(4-Amino-2,7-Dimethyl-7H- Pyrrolo[2,3-D]Pyrimidin-5-Yl)-2,3-Dihydro-1H-Indol-1-Yl]-2-[3-Fluoro- 5-(Trifluoromethyl)Phenyl]Ethanone Inhibitor

All present enzymatic activity of Co-Crystal Structure of Perk Bound to 1-[5-(4-Amino-2,7-Dimethyl-7H- Pyrrolo[2,3-D]Pyrimidin-5-Yl)-2,3-Dihydro-1H-Indol-1-Yl]-2-[3-Fluoro- 5-(Trifluoromethyl)Phenyl]Ethanone Inhibitor:
2.7.11.1;

Protein crystallography data

The structure of Co-Crystal Structure of Perk Bound to 1-[5-(4-Amino-2,7-Dimethyl-7H- Pyrrolo[2,3-D]Pyrimidin-5-Yl)-2,3-Dihydro-1H-Indol-1-Yl]-2-[3-Fluoro- 5-(Trifluoromethyl)Phenyl]Ethanone Inhibitor, PDB code: 4x7o was solved by P.L.Shaffer, A.M.Long, H.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.65
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 125.366, 125.366, 58.203, 90.00, 90.00, 120.00
R / Rfree (%) 19.9 / 22.6

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Co-Crystal Structure of Perk Bound to 1-[5-(4-Amino-2,7-Dimethyl-7H- Pyrrolo[2,3-D]Pyrimidin-5-Yl)-2,3-Dihydro-1H-Indol-1-Yl]-2-[3-Fluoro- 5-(Trifluoromethyl)Phenyl]Ethanone Inhibitor (pdb code 4x7o). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Co-Crystal Structure of Perk Bound to 1-[5-(4-Amino-2,7-Dimethyl-7H- Pyrrolo[2,3-D]Pyrimidin-5-Yl)-2,3-Dihydro-1H-Indol-1-Yl]-2-[3-Fluoro- 5-(Trifluoromethyl)Phenyl]Ethanone Inhibitor, PDB code: 4x7o:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 4x7o

Go back to Fluorine Binding Sites List in 4x7o
Fluorine binding site 1 out of 4 in the Co-Crystal Structure of Perk Bound to 1-[5-(4-Amino-2,7-Dimethyl-7H- Pyrrolo[2,3-D]Pyrimidin-5-Yl)-2,3-Dihydro-1H-Indol-1-Yl]-2-[3-Fluoro- 5-(Trifluoromethyl)Phenyl]Ethanone Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Co-Crystal Structure of Perk Bound to 1-[5-(4-Amino-2,7-Dimethyl-7H- Pyrrolo[2,3-D]Pyrimidin-5-Yl)-2,3-Dihydro-1H-Indol-1-Yl]-2-[3-Fluoro- 5-(Trifluoromethyl)Phenyl]Ethanone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1101

b:73.6
occ:1.00
 F1 A:3Z61101 0.0 73.6 1.0
C23 A:3Z61101 1.3 72.3 1.0
F2 A:3Z61101 2.1 73.7 1.0
F3 A:3Z61101 2.1 71.7 1.0
C9 A:3Z61101 2.4 70.2 1.0
C8 A:3Z61101 2.9 68.1 1.0
CA A:VAL640 3.5 76.8 1.0
CB A:LEU643 3.5 73.7 1.0
C10 A:3Z61101 3.6 65.2 1.0
CB A:VAL640 3.6 76.7 1.0
CD1 A:LEU643 3.8 75.6 1.0
CD1 A:ILE886 3.9 76.0 1.0
O A:VAL640 3.9 71.2 1.0
CG2 A:VAL640 4.2 74.8 1.0
C7 A:3Z61101 4.2 67.3 1.0
C A:VAL640 4.2 75.2 1.0
CG A:LEU643 4.3 76.5 1.0
N A:VAL640 4.6 81.8 1.0
CA A:LEU643 4.6 72.7 1.0
C A:LEU643 4.7 71.5 1.0
N A:ALA644 4.7 73.5 1.0
CG1 A:ILE886 4.7 74.9 1.0
C11 A:3Z61101 4.7 63.8 1.0
CG1 A:VAL640 4.9 80.5 1.0
O A:GLU639 4.9 90.1 1.0
CG2 A:ILE886 4.9 72.2 1.0
C12 A:3Z61101 5.0 64.1 1.0

Fluorine binding site 2 out of 4 in 4x7o

Go back to Fluorine Binding Sites List in 4x7o
Fluorine binding site 2 out of 4 in the Co-Crystal Structure of Perk Bound to 1-[5-(4-Amino-2,7-Dimethyl-7H- Pyrrolo[2,3-D]Pyrimidin-5-Yl)-2,3-Dihydro-1H-Indol-1-Yl]-2-[3-Fluoro- 5-(Trifluoromethyl)Phenyl]Ethanone Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Co-Crystal Structure of Perk Bound to 1-[5-(4-Amino-2,7-Dimethyl-7H- Pyrrolo[2,3-D]Pyrimidin-5-Yl)-2,3-Dihydro-1H-Indol-1-Yl]-2-[3-Fluoro- 5-(Trifluoromethyl)Phenyl]Ethanone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1101

b:73.7
occ:1.00
 F2 A:3Z61101 0.0 73.7 1.0
C23 A:3Z61101 1.3 72.3 1.0
F1 A:3Z61101 2.1 73.6 1.0
F3 A:3Z61101 2.2 71.7 1.0
C9 A:3Z61101 2.4 70.2 1.0
C10 A:3Z61101 2.8 65.2 1.0
O A:VAL640 3.3 71.2 1.0
N A:ALA644 3.3 73.5 1.0
CA A:ALA644 3.5 73.3 1.0
C8 A:3Z61101 3.6 68.1 1.0
CE1 A:TYR654 3.6 63.1 1.0
C A:LEU643 3.6 71.5 1.0
CD1 A:TYR654 3.7 61.5 1.0
CB A:LEU643 3.8 73.7 1.0
CB A:ALA644 3.9 71.4 1.0
O A:LEU643 4.0 69.3 1.0
CZ A:TYR654 4.1 65.6 1.0
C11 A:3Z61101 4.1 63.8 1.0
C A:VAL640 4.2 75.2 1.0
CG2 A:VAL640 4.2 74.8 1.0
CA A:VAL640 4.2 76.8 1.0
CG A:TYR654 4.2 60.6 1.0
CA A:LEU643 4.3 72.7 1.0
CB A:VAL640 4.3 76.7 1.0
CE2 A:TYR654 4.6 63.7 1.0
CD2 A:TYR654 4.6 61.6 1.0
OH A:TYR654 4.7 67.1 1.0
C7 A:3Z61101 4.7 67.3 1.0
C A:ALA644 4.9 73.4 1.0
C12 A:3Z61101 5.0 64.1 1.0
N A:LEU643 5.0 72.9 1.0

Fluorine binding site 3 out of 4 in 4x7o

Go back to Fluorine Binding Sites List in 4x7o
Fluorine binding site 3 out of 4 in the Co-Crystal Structure of Perk Bound to 1-[5-(4-Amino-2,7-Dimethyl-7H- Pyrrolo[2,3-D]Pyrimidin-5-Yl)-2,3-Dihydro-1H-Indol-1-Yl]-2-[3-Fluoro- 5-(Trifluoromethyl)Phenyl]Ethanone Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Co-Crystal Structure of Perk Bound to 1-[5-(4-Amino-2,7-Dimethyl-7H- Pyrrolo[2,3-D]Pyrimidin-5-Yl)-2,3-Dihydro-1H-Indol-1-Yl]-2-[3-Fluoro- 5-(Trifluoromethyl)Phenyl]Ethanone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1101

b:71.7
occ:1.00
 F3 A:3Z61101 0.0 71.7 1.0
C23 A:3Z61101 1.3 72.3 1.0
F1 A:3Z61101 2.1 73.6 1.0
F2 A:3Z61101 2.2 73.7 1.0
C9 A:3Z61101 2.3 70.2 1.0
C8 A:3Z61101 3.1 68.1 1.0
CG2 A:ILE886 3.2 72.2 1.0
C10 A:3Z61101 3.3 65.2 1.0
CD1 A:TYR654 3.4 61.5 1.0
CE1 A:TYR654 3.4 63.1 1.0
CD1 A:ILE886 3.5 76.0 1.0
CG1 A:ILE886 3.7 74.9 1.0
CB A:ILE886 4.1 72.0 1.0
C7 A:3Z61101 4.3 67.3 1.0
SD A:MET888 4.3 62.3 1.0
CZ A:TYR654 4.5 65.6 1.0
CG A:TYR654 4.5 60.6 1.0
C11 A:3Z61101 4.5 63.8 1.0
CB A:ALA657 4.8 70.0 1.0
CB A:VAL640 4.8 76.7 1.0
CG2 A:VAL640 4.8 74.8 1.0
C12 A:3Z61101 5.0 64.1 1.0

Fluorine binding site 4 out of 4 in 4x7o

Go back to Fluorine Binding Sites List in 4x7o
Fluorine binding site 4 out of 4 in the Co-Crystal Structure of Perk Bound to 1-[5-(4-Amino-2,7-Dimethyl-7H- Pyrrolo[2,3-D]Pyrimidin-5-Yl)-2,3-Dihydro-1H-Indol-1-Yl]-2-[3-Fluoro- 5-(Trifluoromethyl)Phenyl]Ethanone Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Co-Crystal Structure of Perk Bound to 1-[5-(4-Amino-2,7-Dimethyl-7H- Pyrrolo[2,3-D]Pyrimidin-5-Yl)-2,3-Dihydro-1H-Indol-1-Yl]-2-[3-Fluoro- 5-(Trifluoromethyl)Phenyl]Ethanone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1101

b:62.9
occ:1.00
 F4 A:3Z61101 0.0 62.9 1.0
C11 A:3Z61101 1.3 63.8 1.0
C12 A:3Z61101 2.3 64.1 1.0
C10 A:3Z61101 2.4 65.2 1.0
O A:HOH1202 3.2 63.9 1.0
O A:LEU643 3.3 69.3 1.0
C7 A:3Z61101 3.6 67.3 1.0
C9 A:3Z61101 3.7 70.2 1.0
CB A:TYR654 3.7 60.5 1.0
O A:LEU646 3.8 69.1 1.0
CG2 A:ILE651 3.9 59.2 1.0
CB A:LEU646 3.9 72.0 1.0
O A:VAL652 4.0 66.2 1.0
C8 A:3Z61101 4.1 68.1 1.0
CE A:MET888 4.2 57.3 1.0
C A:LEU643 4.3 71.5 1.0
C A:LEU646 4.6 71.6 1.0
CG A:TYR654 4.6 60.6 1.0
CA A:LEU646 4.6 73.4 1.0
N A:TYR654 4.7 60.3 1.0
CD1 A:LEU646 4.7 73.1 1.0
CA A:TYR654 4.7 61.1 1.0
CG A:LEU646 4.8 73.6 1.0
N A:LEU646 4.8 72.5 1.0
C22 A:3Z61101 4.9 60.7 1.0
C23 A:3Z61101 5.0 72.3 1.0

Reference:

A.L.Smith, K.L.Andrews, H.Beckmann, S.F.Bellon, P.J.Beltran, S.Booker, H.Chen, Y.A.Chung, N.D.D'angelo, J.Dao, K.R.Dellamaggiore, P.Jaeckel, R.Kendall, K.Labitzke, A.M.Long, S.Materna-Reichelt, P.Mitchell, M.H.Norman, D.Powers, M.Rose, P.L.Shaffer, M.M.Wu, J.R.Lipford. Discovery of 1H-Pyrazol-3(2H)-Ones As Potent and Selective Inhibitors of Protein Kinase R-Like Endoplasmic Reticulum Kinase (Perk). J.Med.Chem. 2015.
ISSN: ISSN 0022-2623
PubMed: 25587754
DOI: 10.1021/JM5017494
Page generated: Thu Aug 1 06:40:29 2024

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