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Fluorine in PDB 3n3g: 4-(3-Trifluoromethylphenyl)-Pyrimidine-2-Carbonitrile As Cathepsin S Inhibitors: N3, Not N1 Is Critically Important

Enzymatic activity of 4-(3-Trifluoromethylphenyl)-Pyrimidine-2-Carbonitrile As Cathepsin S Inhibitors: N3, Not N1 Is Critically Important

All present enzymatic activity of 4-(3-Trifluoromethylphenyl)-Pyrimidine-2-Carbonitrile As Cathepsin S Inhibitors: N3, Not N1 Is Critically Important:
3.4.22.27;

Protein crystallography data

The structure of 4-(3-Trifluoromethylphenyl)-Pyrimidine-2-Carbonitrile As Cathepsin S Inhibitors: N3, Not N1 Is Critically Important, PDB code: 3n3g was solved by X.Fradera, J.C.M.Uitdehaag, M.Van Zeeland, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 74.56 / 1.60
Space group P 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 85.757, 85.757, 150.902, 90.00, 90.00, 90.00
R / Rfree (%) 22.3 / 26.4

Fluorine Binding Sites:

The binding sites of Fluorine atom in the 4-(3-Trifluoromethylphenyl)-Pyrimidine-2-Carbonitrile As Cathepsin S Inhibitors: N3, Not N1 Is Critically Important (pdb code 3n3g). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 9 binding sites of Fluorine where determined in the 4-(3-Trifluoromethylphenyl)-Pyrimidine-2-Carbonitrile As Cathepsin S Inhibitors: N3, Not N1 Is Critically Important, PDB code: 3n3g:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 3n3g

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Fluorine binding site 1 out of 9 in the 4-(3-Trifluoromethylphenyl)-Pyrimidine-2-Carbonitrile As Cathepsin S Inhibitors: N3, Not N1 Is Critically Important


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of 4-(3-Trifluoromethylphenyl)-Pyrimidine-2-Carbonitrile As Cathepsin S Inhibitors: N3, Not N1 Is Critically Important within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F220

b:30.1
occ:0.75
 F21 A:935220 0.0 30.1 0.8
C20 A:935220 1.3 31.3 0.8
F22 A:935220 2.1 31.0 0.8
F23 A:935220 2.2 32.6 0.8
C9 A:935220 2.3 31.4 0.8
O13 A:935220 2.8 31.0 0.8
C10 A:935220 2.9 31.9 0.8
C8 A:935220 3.4 30.9 0.8
O A:GLY69 3.7 21.0 1.0
C14 A:935220 3.9 29.7 0.8
SD A:MET71 3.9 18.4 1.0
O A:HOH305 4.0 26.6 1.0
C15 A:935220 4.1 28.6 0.8
CE A:MET71 4.1 15.7 1.0
C11 A:935220 4.2 32.0 0.8
CA A:PHE70 4.2 21.1 1.0
CD2 A:PHE70 4.4 25.6 1.0
C7 A:935220 4.6 32.0 0.8
N A:MET71 4.7 19.8 1.0
C A:GLY69 4.7 20.3 1.0
CB A:PHE70 4.8 22.1 1.0
C12 A:935220 4.9 31.5 0.8
CG A:PHE70 4.9 23.3 1.0
N A:PHE70 5.0 20.6 1.0

Fluorine binding site 2 out of 9 in 3n3g

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Fluorine binding site 2 out of 9 in the 4-(3-Trifluoromethylphenyl)-Pyrimidine-2-Carbonitrile As Cathepsin S Inhibitors: N3, Not N1 Is Critically Important


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of 4-(3-Trifluoromethylphenyl)-Pyrimidine-2-Carbonitrile As Cathepsin S Inhibitors: N3, Not N1 Is Critically Important within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F220

b:31.0
occ:0.75
 F22 A:935220 0.0 31.0 0.8
C20 A:935220 1.3 31.3 0.8
F23 A:935220 2.1 32.6 0.8
F21 A:935220 2.1 30.1 0.8
C9 A:935220 2.4 31.4 0.8
O13 A:935220 3.0 31.0 0.8
C10 A:935220 3.0 31.9 0.8
CA A:GLY137 3.2 20.8 1.0
C8 A:935220 3.4 30.9 0.8
O A:HIS164 4.0 20.9 1.0
N A:GLY137 4.0 20.2 1.0
CG2 A:VAL162 4.0 23.3 1.0
C A:HIS164 4.0 20.8 1.0
N A:GLY165 4.1 20.4 1.0
CA A:GLY165 4.2 19.6 1.0
CE A:MET71 4.2 15.7 1.0
N A:HIS164 4.3 21.4 1.0
C11 A:935220 4.3 32.0 0.8
C14 A:935220 4.4 29.7 0.8
C A:GLY137 4.4 20.9 1.0
SD A:MET71 4.5 18.4 1.0
CB A:VAL162 4.5 23.6 1.0
C7 A:935220 4.6 32.0 0.8
O A:VAL136 4.6 20.3 1.0
C A:VAL136 4.7 19.9 1.0
N A:VAL138 4.7 21.4 1.0
C15 A:935220 4.7 28.6 0.8
CA A:HIS164 4.7 21.1 1.0
N A:ASN163 4.9 23.0 1.0
C A:ASN163 4.9 22.4 1.0
C A:VAL162 4.9 23.3 1.0
C12 A:935220 5.0 31.5 0.8

Fluorine binding site 3 out of 9 in 3n3g

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Fluorine binding site 3 out of 9 in the 4-(3-Trifluoromethylphenyl)-Pyrimidine-2-Carbonitrile As Cathepsin S Inhibitors: N3, Not N1 Is Critically Important


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of 4-(3-Trifluoromethylphenyl)-Pyrimidine-2-Carbonitrile As Cathepsin S Inhibitors: N3, Not N1 Is Critically Important within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F220

b:32.6
occ:0.75
 F23 A:935220 0.0 32.6 0.8
C20 A:935220 1.3 31.3 0.8
F22 A:935220 2.1 31.0 0.8
F21 A:935220 2.2 30.1 0.8
C9 A:935220 2.3 31.4 0.8
C8 A:935220 2.6 30.9 0.8
SD A:MET71 3.3 18.4 1.0
CA A:GLY165 3.3 19.6 1.0
N A:GLY165 3.4 20.4 1.0
C10 A:935220 3.6 31.9 0.8
O A:GLY69 3.8 21.0 1.0
CE A:MET71 3.9 15.7 1.0
C A:HIS164 4.0 20.8 1.0
C7 A:935220 4.0 32.0 0.8
O13 A:935220 4.1 31.0 0.8
CB A:TRP26 4.2 20.4 1.0
O A:HIS164 4.4 20.9 1.0
CA A:TRP26 4.6 20.2 1.0
CA A:GLY137 4.7 20.8 1.0
CA A:HIS164 4.7 21.1 1.0
C11 A:935220 4.7 32.0 0.8
N A:HIS164 4.7 21.4 1.0
SG A:CYS25 4.8 23.5 1.0
C A:GLY165 4.8 19.2 1.0
N1 A:935220 4.8 32.4 0.8
C12 A:935220 4.9 31.5 0.8
C2 A:935220 4.9 31.9 0.8
C A:GLY69 5.0 20.3 1.0

Fluorine binding site 4 out of 9 in 3n3g

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Fluorine binding site 4 out of 9 in the 4-(3-Trifluoromethylphenyl)-Pyrimidine-2-Carbonitrile As Cathepsin S Inhibitors: N3, Not N1 Is Critically Important


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of 4-(3-Trifluoromethylphenyl)-Pyrimidine-2-Carbonitrile As Cathepsin S Inhibitors: N3, Not N1 Is Critically Important within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F221

b:23.6
occ:0.75
 F21 A:93N221 0.0 23.6 0.8
C20 A:93N221 1.4 23.6 0.8
F22 A:93N221 2.1 23.2 0.8
F23 A:93N221 2.1 24.1 0.8
C9 A:93N221 2.4 23.5 0.8
O A:PHE146 2.9 23.6 1.0
O13 A:93N221 2.9 25.1 0.8
C26 A:93N221 3.0 35.2 0.8
C10 A:93N221 3.1 24.1 0.8
C27 A:93N221 3.5 34.9 0.8
N17 A:93N221 3.6 34.4 0.8
C8 A:93N221 3.6 23.3 0.8
O A:HOH324 3.6 22.7 1.0
C24 A:93N221 3.7 35.5 0.8
C A:PHE146 3.8 23.2 1.0
N25 A:93N221 3.9 35.7 0.8
C14 A:93N221 4.1 28.3 0.8
CA A:LEU147 4.2 23.6 1.0
C28 A:93N221 4.2 34.5 0.8
N A:LEU147 4.4 23.2 1.0
C11 A:93N221 4.4 23.9 0.8
CD2 A:LEU147 4.4 24.6 1.0
C29 A:93N221 4.5 35.0 0.8
C16 A:93N221 4.7 32.3 0.8
C7 A:93N221 4.8 22.4 0.8
C15 A:93N221 4.8 30.2 0.8
CA A:PHE146 4.9 23.1 1.0
C A:LEU147 4.9 23.7 1.0

Fluorine binding site 5 out of 9 in 3n3g

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Fluorine binding site 5 out of 9 in the 4-(3-Trifluoromethylphenyl)-Pyrimidine-2-Carbonitrile As Cathepsin S Inhibitors: N3, Not N1 Is Critically Important


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of 4-(3-Trifluoromethylphenyl)-Pyrimidine-2-Carbonitrile As Cathepsin S Inhibitors: N3, Not N1 Is Critically Important within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F221

b:23.2
occ:0.75
 F22 A:93N221 0.0 23.2 0.8
C20 A:93N221 1.4 23.6 0.8
F21 A:93N221 2.1 23.6 0.8
F23 A:93N221 2.1 24.1 0.8
C9 A:93N221 2.4 23.5 0.8
C8 A:93N221 2.8 23.3 0.8
O A:PHE146 3.4 23.6 1.0
C10 A:93N221 3.7 24.1 0.8
C A:PHE146 3.9 23.2 1.0
CB A:PHE146 3.9 23.2 1.0
C7 A:93N221 4.2 22.4 0.8
O13 A:93N221 4.2 25.1 0.8
CA A:PHE146 4.4 23.1 1.0
CD2 A:PHE146 4.5 23.4 1.0
CD2 A:LEU147 4.6 24.6 1.0
N A:LEU147 4.7 23.2 1.0
CG A:PHE146 4.7 23.9 1.0
C11 A:93N221 4.8 23.9 0.8
CA A:LEU147 5.0 23.6 1.0
C12 A:93N221 5.0 23.7 0.8

Fluorine binding site 6 out of 9 in 3n3g

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Fluorine binding site 6 out of 9 in the 4-(3-Trifluoromethylphenyl)-Pyrimidine-2-Carbonitrile As Cathepsin S Inhibitors: N3, Not N1 Is Critically Important


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of 4-(3-Trifluoromethylphenyl)-Pyrimidine-2-Carbonitrile As Cathepsin S Inhibitors: N3, Not N1 Is Critically Important within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F221

b:24.1
occ:0.75
 F23 A:93N221 0.0 24.1 0.8
C20 A:93N221 1.3 23.6 0.8
F22 A:93N221 2.1 23.2 0.8
F21 A:93N221 2.1 23.6 0.8
C9 A:93N221 2.4 23.5 0.8
O13 A:93N221 3.1 25.1 0.8
C10 A:93N221 3.1 24.1 0.8
C8 A:93N221 3.4 23.3 0.8
C14 A:93N221 3.8 28.3 0.8
N17 A:93N221 3.9 34.4 0.8
C3 A:PEG218 3.9 44.9 0.5
C4 A:PEG218 4.2 44.7 0.5
C24 A:93N221 4.2 35.5 0.8
C28 A:93N221 4.3 34.5 0.8
O2 A:PEG218 4.3 45.4 0.5
C11 A:93N221 4.4 23.9 0.8
C26 A:93N221 4.5 35.2 0.8
C27 A:93N221 4.6 34.9 0.8
C7 A:93N221 4.6 22.4 0.8
C16 A:93N221 4.7 32.3 0.8
O A:PHE146 4.8 23.6 1.0
C15 A:93N221 4.8 30.2 0.8

Fluorine binding site 7 out of 9 in 3n3g

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Fluorine binding site 7 out of 9 in the 4-(3-Trifluoromethylphenyl)-Pyrimidine-2-Carbonitrile As Cathepsin S Inhibitors: N3, Not N1 Is Critically Important


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of 4-(3-Trifluoromethylphenyl)-Pyrimidine-2-Carbonitrile As Cathepsin S Inhibitors: N3, Not N1 Is Critically Important within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F221

b:35.7
occ:0.75
 F21 B:935221 0.0 35.7 0.8
C20 B:935221 1.3 35.1 0.8
F22 B:935221 2.1 35.1 0.8
F23 B:935221 2.1 35.8 0.8
C9 B:935221 2.3 35.4 0.8
O13 B:935221 2.8 34.9 0.8
C10 B:935221 2.9 35.1 0.8
C8 B:935221 3.4 34.5 0.8
SD B:MET71 3.9 20.1 1.0
O B:GLY69 4.0 22.4 1.0
CE B:MET71 4.0 20.6 1.0
C14 B:935221 4.0 34.7 0.8
C11 B:935221 4.3 35.0 0.8
C15 B:935221 4.3 33.7 0.8
CD2 B:PHE70 4.3 28.3 1.0
CA B:PHE70 4.4 23.5 1.0
C7 B:935221 4.6 35.0 0.8
N B:MET71 4.8 21.8 1.0
CB B:PHE70 4.9 24.9 1.0
C12 B:935221 4.9 35.0 0.8
C B:GLY69 5.0 22.6 1.0

Fluorine binding site 8 out of 9 in 3n3g

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Fluorine binding site 8 out of 9 in the 4-(3-Trifluoromethylphenyl)-Pyrimidine-2-Carbonitrile As Cathepsin S Inhibitors: N3, Not N1 Is Critically Important


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of 4-(3-Trifluoromethylphenyl)-Pyrimidine-2-Carbonitrile As Cathepsin S Inhibitors: N3, Not N1 Is Critically Important within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F221

b:35.1
occ:0.75
 F22 B:935221 0.0 35.1 0.8
C20 B:935221 1.3 35.1 0.8
F21 B:935221 2.1 35.7 0.8
F23 B:935221 2.2 35.8 0.8
C9 B:935221 2.3 35.4 0.8
O13 B:935221 2.9 34.9 0.8
C10 B:935221 2.9 35.1 0.8
CA B:GLY137 3.3 19.4 1.0
C8 B:935221 3.4 34.5 0.8
CG2 B:VAL162 3.8 21.6 1.0
N B:GLY137 4.0 19.4 1.0
O B:HIS164 4.1 21.5 1.0
CE B:MET71 4.2 20.6 1.0
C B:HIS164 4.2 20.6 1.0
C11 B:935221 4.2 35.0 0.8
C14 B:935221 4.2 34.7 0.8
N B:GLY165 4.3 20.8 1.0
CA B:GLY165 4.4 20.4 1.0
N B:HIS164 4.4 21.1 1.0
SD B:MET71 4.5 20.1 1.0
CB B:VAL162 4.5 22.2 1.0
C B:GLY137 4.5 19.5 1.0
C7 B:935221 4.5 35.0 0.8
C15 B:935221 4.7 33.7 0.8
O B:VAL136 4.7 19.5 1.0
C B:VAL136 4.7 19.3 1.0
N B:VAL138 4.9 19.6 1.0
C12 B:935221 4.9 35.0 0.8
CA B:HIS164 4.9 20.9 1.0
C B:VAL162 5.0 22.8 1.0

Fluorine binding site 9 out of 9 in 3n3g

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Fluorine binding site 9 out of 9 in the 4-(3-Trifluoromethylphenyl)-Pyrimidine-2-Carbonitrile As Cathepsin S Inhibitors: N3, Not N1 Is Critically Important


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of 4-(3-Trifluoromethylphenyl)-Pyrimidine-2-Carbonitrile As Cathepsin S Inhibitors: N3, Not N1 Is Critically Important within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F221

b:35.8
occ:0.75
 F23 B:935221 0.0 35.8 0.8
C20 B:935221 1.3 35.1 0.8
F21 B:935221 2.1 35.7 0.8
F22 B:935221 2.2 35.1 0.8
C9 B:935221 2.3 35.4 0.8
C8 B:935221 2.6 34.5 0.8
SD B:MET71 3.2 20.1 1.0
CA B:GLY165 3.4 20.4 1.0
N B:GLY165 3.5 20.8 1.0
C10 B:935221 3.6 35.1 0.8
CE B:MET71 3.7 20.6 1.0
C7 B:935221 4.0 35.0 0.8
O B:GLY69 4.0 22.4 1.0
C B:HIS164 4.0 20.6 1.0
O13 B:935221 4.1 34.9 0.8
CB B:TRP26 4.3 20.0 1.0
O B:HIS164 4.4 21.5 1.0
CA B:TRP26 4.6 20.4 1.0
C11 B:935221 4.7 35.0 0.8
CA B:GLY137 4.7 19.4 1.0
N1 B:935221 4.7 35.9 0.8
CA B:HIS164 4.8 20.9 1.0
C12 B:935221 4.8 35.0 0.8
C2 B:935221 4.8 35.1 0.8
N B:HIS164 4.9 21.1 1.0
C B:GLY165 4.9 20.5 1.0
CG B:MET71 5.0 20.5 1.0
O B:VAL136 5.0 19.5 1.0

Reference:

J.Cai, X.Fradera, M.Van Zeeland, M.Dempster, K.S.Cameron, D.J.Bennett, J.Robinson, L.Popplestone, M.Baugh, P.Westwood, J.Bruin, W.Hamilton, E.Kinghorn, C.Long, J.C.Uitdehaag. 4-(3-Trifluoromethylphenyl)-Pyrimidine-2-Carbonitrile As Cathepsin S Inhibitors: N3, Not N1 Is Critically Important. Bioorg.Med.Chem.Lett. V. 20 4507 2010.
ISSN: ISSN 0960-894X
PubMed: 20580231
DOI: 10.1016/J.BMCL.2010.06.043
Page generated: Sun Dec 13 11:51:12 2020

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