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Fluorine in PDB 4x7j: Co-Crystal Structure of Perk with 2-Amino-N-[4-Methoxy-3- (Trifluoromethyl)Phenyl]-4-Methyl-3-[2-(Methylamino)Quinazolin-6- Yl]Benzamide Inhibitor

Enzymatic activity of Co-Crystal Structure of Perk with 2-Amino-N-[4-Methoxy-3- (Trifluoromethyl)Phenyl]-4-Methyl-3-[2-(Methylamino)Quinazolin-6- Yl]Benzamide Inhibitor

All present enzymatic activity of Co-Crystal Structure of Perk with 2-Amino-N-[4-Methoxy-3- (Trifluoromethyl)Phenyl]-4-Methyl-3-[2-(Methylamino)Quinazolin-6- Yl]Benzamide Inhibitor:
2.7.11.1;

Protein crystallography data

The structure of Co-Crystal Structure of Perk with 2-Amino-N-[4-Methoxy-3- (Trifluoromethyl)Phenyl]-4-Methyl-3-[2-(Methylamino)Quinazolin-6- Yl]Benzamide Inhibitor, PDB code: 4x7j 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) 42.64 / 2.30
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 81.020, 81.020, 127.617, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 22.5

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Co-Crystal Structure of Perk with 2-Amino-N-[4-Methoxy-3- (Trifluoromethyl)Phenyl]-4-Methyl-3-[2-(Methylamino)Quinazolin-6- Yl]Benzamide Inhibitor (pdb code 4x7j). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Co-Crystal Structure of Perk with 2-Amino-N-[4-Methoxy-3- (Trifluoromethyl)Phenyl]-4-Methyl-3-[2-(Methylamino)Quinazolin-6- Yl]Benzamide Inhibitor, PDB code: 4x7j:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 4x7j

Go back to Fluorine Binding Sites List in 4x7j
Fluorine binding site 1 out of 3 in the Co-Crystal Structure of Perk with 2-Amino-N-[4-Methoxy-3- (Trifluoromethyl)Phenyl]-4-Methyl-3-[2-(Methylamino)Quinazolin-6- Yl]Benzamide 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 with 2-Amino-N-[4-Methoxy-3- (Trifluoromethyl)Phenyl]-4-Methyl-3-[2-(Methylamino)Quinazolin-6- Yl]Benzamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1101

b:56.0
occ:1.00
 F34 A:3Z11101 0.0 56.0 1.0
C32 A:3Z11101 1.3 54.9 1.0
F35 A:3Z11101 2.2 56.5 1.0
F33 A:3Z11101 2.2 54.3 1.0
C28 A:3Z11101 2.3 53.2 1.0
O30 A:3Z11101 2.9 56.1 1.0
C27 A:3Z11101 2.9 53.9 1.0
CD1 A:LEU646 3.1 37.9 1.0
C29 A:3Z11101 3.4 49.0 1.0
C31 A:3Z11101 3.5 54.3 1.0
CD2 A:LEU928 3.6 38.1 1.0
C26 A:3Z11101 4.2 52.6 1.0
CG2 A:ILE651 4.3 32.4 1.0
CD1 A:LEU643 4.4 35.4 1.0
CD1 A:ILE651 4.4 33.7 1.0
C24 A:3Z11101 4.6 47.8 1.0
CG A:LEU646 4.6 37.8 1.0
CD1 A:LEU928 4.7 36.7 1.0
CG A:LEU928 4.7 37.6 1.0
C25 A:3Z11101 4.9 50.2 1.0
CD2 A:LEU933 4.9 53.9 1.0

Fluorine binding site 2 out of 3 in 4x7j

Go back to Fluorine Binding Sites List in 4x7j
Fluorine binding site 2 out of 3 in the Co-Crystal Structure of Perk with 2-Amino-N-[4-Methoxy-3- (Trifluoromethyl)Phenyl]-4-Methyl-3-[2-(Methylamino)Quinazolin-6- Yl]Benzamide 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 with 2-Amino-N-[4-Methoxy-3- (Trifluoromethyl)Phenyl]-4-Methyl-3-[2-(Methylamino)Quinazolin-6- Yl]Benzamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1101

b:56.5
occ:1.00
 F35 A:3Z11101 0.0 56.5 1.0
C32 A:3Z11101 1.3 54.9 1.0
F34 A:3Z11101 2.2 56.0 1.0
F33 A:3Z11101 2.2 54.3 1.0
C28 A:3Z11101 2.4 53.2 1.0
C29 A:3Z11101 2.7 49.0 1.0
CA A:GLY954 3.4 39.1 1.0
C27 A:3Z11101 3.7 53.9 1.0
O A:VAL953 3.9 38.5 1.0
C24 A:3Z11101 4.1 47.8 1.0
CD1 A:ILE651 4.2 33.7 1.0
O30 A:3Z11101 4.2 56.1 1.0
C A:GLY954 4.2 39.7 1.0
O22 A:3Z11101 4.2 37.3 1.0
N A:GLY954 4.2 38.5 1.0
CG2 A:ILE651 4.3 32.4 1.0
C A:VAL953 4.4 37.8 1.0
N A:ASP955 4.4 40.8 1.0
CD2 A:LEU928 4.7 38.1 1.0
CD2 A:HIS935 4.7 54.6 1.0
CD1 A:LEU928 4.8 36.7 1.0
C26 A:3Z11101 4.8 52.6 1.0
CD1 A:LEU643 5.0 35.4 1.0
C25 A:3Z11101 5.0 50.2 1.0
N23 A:3Z11101 5.0 44.8 1.0
O A:GLY954 5.0 39.4 1.0
C21 A:3Z11101 5.0 39.5 1.0

Fluorine binding site 3 out of 3 in 4x7j

Go back to Fluorine Binding Sites List in 4x7j
Fluorine binding site 3 out of 3 in the Co-Crystal Structure of Perk with 2-Amino-N-[4-Methoxy-3- (Trifluoromethyl)Phenyl]-4-Methyl-3-[2-(Methylamino)Quinazolin-6- Yl]Benzamide 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 with 2-Amino-N-[4-Methoxy-3- (Trifluoromethyl)Phenyl]-4-Methyl-3-[2-(Methylamino)Quinazolin-6- Yl]Benzamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1101

b:54.3
occ:1.00
 F33 A:3Z11101 0.0 54.3 1.0
C32 A:3Z11101 1.3 54.9 1.0
F34 A:3Z11101 2.2 56.0 1.0
F35 A:3Z11101 2.2 56.5 1.0
C28 A:3Z11101 2.3 53.2 1.0
O30 A:3Z11101 2.8 56.1 1.0
C27 A:3Z11101 2.9 53.9 1.0
C29 A:3Z11101 3.5 49.0 1.0
CD2 A:LEU928 4.0 38.1 1.0
C31 A:3Z11101 4.0 54.3 1.0
CD1 A:LEU928 4.1 36.7 1.0
CD2 A:HIS935 4.2 54.6 1.0
C26 A:3Z11101 4.2 52.6 1.0
C24 A:3Z11101 4.6 47.8 1.0
CG A:LEU928 4.7 37.6 1.0
NE2 A:HIS935 4.8 55.8 1.0
CG A:HIS935 4.9 54.6 1.0
CA A:GLY954 4.9 39.1 1.0
C25 A:3Z11101 4.9 50.2 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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