Atomistry » Fluorine » PDB 3n2m-3nly » 3n3g
Atomistry »
  Fluorine »
    PDB 3n2m-3nly »
      3n3g »

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

Go back to Fluorine Binding Sites List in 3n3g
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

Go back to Fluorine Binding Sites List in 3n3g
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

Go back to Fluorine Binding Sites List in 3n3g
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

Go back to Fluorine Binding Sites List in 3n3g
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

Go back to Fluorine Binding Sites List in 3n3g
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

Go back to Fluorine Binding Sites List in 3n3g
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

Go back to Fluorine Binding Sites List in 3n3g
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

Go back to Fluorine Binding Sites List in 3n3g
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

Go back to Fluorine Binding Sites List in 3n3g
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: Wed Jul 31 20:50:01 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy