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Fluorine in PDB 3n4c: 6-Phenyl-1H-Imidazo[4,5-C]Pyridine-4-Carbonitrile As Cathepsin S Inhibitors

Enzymatic activity of 6-Phenyl-1H-Imidazo[4,5-C]Pyridine-4-Carbonitrile As Cathepsin S Inhibitors

All present enzymatic activity of 6-Phenyl-1H-Imidazo[4,5-C]Pyridine-4-Carbonitrile As Cathepsin S Inhibitors:
3.4.22.27;

Protein crystallography data

The structure of 6-Phenyl-1H-Imidazo[4,5-C]Pyridine-4-Carbonitrile As Cathepsin S Inhibitors, PDB code: 3n4c 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) 56.54 / 1.90
Space group P 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 85.629, 85.629, 150.573, 90.00, 90.00, 90.00
R / Rfree (%) 24.9 / 28.6

Fluorine Binding Sites:

The binding sites of Fluorine atom in the 6-Phenyl-1H-Imidazo[4,5-C]Pyridine-4-Carbonitrile As Cathepsin S Inhibitors (pdb code 3n4c). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the 6-Phenyl-1H-Imidazo[4,5-C]Pyridine-4-Carbonitrile As Cathepsin S Inhibitors, PDB code: 3n4c:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3n4c

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Fluorine binding site 1 out of 6 in the 6-Phenyl-1H-Imidazo[4,5-C]Pyridine-4-Carbonitrile As Cathepsin S Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of 6-Phenyl-1H-Imidazo[4,5-C]Pyridine-4-Carbonitrile As Cathepsin S Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F218

b:38.8
occ:1.00
 F23 A:EF3218 0.0 38.8 1.0
C22 A:EF3218 1.4 38.6 1.0
F25 A:EF3218 2.2 35.2 1.0
F24 A:EF3218 2.2 38.5 1.0
C6 A:EF3218 2.4 38.8 1.0
O17 A:EF3218 2.9 41.1 1.0
CE2 A:PHE211 3.0 19.4 0.5
C7 A:EF3218 3.0 39.4 1.0
O A:GLY69 3.5 18.3 1.0
C11 A:EF3218 3.5 38.9 1.0
CD2 A:PHE211 3.7 19.9 0.5
SD A:MET71 3.9 18.0 1.0
CZ A:PHE211 3.9 20.1 0.5
CA A:PHE70 4.0 19.7 1.0
CE A:MET71 4.0 21.3 1.0
CD2 A:PHE70 4.0 27.5 1.0
C18 A:EF3218 4.1 46.0 1.0
C8 A:EF3218 4.3 39.5 1.0
C20 A:EF3218 4.4 49.8 1.0
C A:GLY69 4.4 19.3 1.0
N A:MET71 4.5 17.0 1.0
CB A:PHE70 4.6 21.3 1.0
C10 A:EF3218 4.7 38.7 1.0
N A:PHE70 4.7 19.3 1.0
CG A:PHE70 4.8 22.6 1.0
C19 A:EF3218 4.8 47.2 1.0
C A:PHE70 4.8 18.5 1.0
C32 A:EF3218 4.8 53.6 1.0
CE2 A:PHE70 4.9 26.1 1.0
N21 A:EF3218 4.9 52.1 1.0

Fluorine binding site 2 out of 6 in 3n4c

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Fluorine binding site 2 out of 6 in the 6-Phenyl-1H-Imidazo[4,5-C]Pyridine-4-Carbonitrile As Cathepsin S Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of 6-Phenyl-1H-Imidazo[4,5-C]Pyridine-4-Carbonitrile As Cathepsin S Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F218

b:38.5
occ:1.00
 F24 A:EF3218 0.0 38.5 1.0
C22 A:EF3218 1.4 38.6 1.0
F25 A:EF3218 2.2 35.2 1.0
F23 A:EF3218 2.2 38.8 1.0
C6 A:EF3218 2.4 38.8 1.0
O17 A:EF3218 2.8 41.1 1.0
C7 A:EF3218 3.0 39.4 1.0
CA A:GLY137 3.5 16.8 1.0
C11 A:EF3218 3.5 38.9 1.0
CD2 A:PHE211 3.6 19.9 0.5
CG2 A:VAL162 3.7 23.5 1.0
CE2 A:PHE211 3.7 19.4 0.5
C18 A:EF3218 4.2 46.0 1.0
N A:GLY137 4.2 16.9 1.0
CB A:VAL162 4.3 23.7 1.0
C8 A:EF3218 4.3 39.5 1.0
CE A:MET71 4.4 21.3 1.0
O A:HIS164 4.4 20.0 1.0
C20 A:EF3218 4.4 49.8 1.0
C A:HIS164 4.5 18.9 1.0
C19 A:EF3218 4.5 47.2 1.0
N A:HIS164 4.6 19.7 1.0
C A:GLY137 4.6 17.5 1.0
N A:GLY165 4.7 18.1 1.0
C A:VAL162 4.7 22.9 1.0
N A:ASN163 4.7 22.8 1.0
C10 A:EF3218 4.7 38.7 1.0
CA A:GLY165 4.7 18.1 1.0
O A:VAL162 4.8 21.1 1.0
SD A:MET71 4.9 18.0 1.0
CG A:PHE211 4.9 20.6 0.5
N A:VAL138 5.0 17.8 1.0
C A:ASN163 5.0 20.9 1.0

Fluorine binding site 3 out of 6 in 3n4c

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Fluorine binding site 3 out of 6 in the 6-Phenyl-1H-Imidazo[4,5-C]Pyridine-4-Carbonitrile As Cathepsin S Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of 6-Phenyl-1H-Imidazo[4,5-C]Pyridine-4-Carbonitrile As Cathepsin S Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F218

b:35.2
occ:1.00
 F25 A:EF3218 0.0 35.2 1.0
C22 A:EF3218 1.4 38.6 1.0
F23 A:EF3218 2.2 38.8 1.0
F24 A:EF3218 2.2 38.5 1.0
C6 A:EF3218 2.4 38.8 1.0
C11 A:EF3218 2.8 38.9 1.0
CA A:GLY165 3.3 18.1 1.0
N A:GLY165 3.3 18.1 1.0
SD A:MET71 3.5 18.0 1.0
C7 A:EF3218 3.7 39.4 1.0
C A:HIS164 3.7 18.9 1.0
CE A:MET71 3.8 21.3 1.0
O A:GLY69 4.0 18.3 1.0
O A:HIS164 4.1 20.0 1.0
O17 A:EF3218 4.1 41.1 1.0
C10 A:EF3218 4.2 38.7 1.0
CA A:GLY137 4.4 16.8 1.0
CB A:TRP26 4.4 17.5 1.0
CA A:HIS164 4.5 19.3 1.0
CE2 A:PHE211 4.5 19.4 0.5
N A:HIS164 4.5 19.7 1.0
N15 A:EF3218 4.7 37.3 1.0
C A:GLY165 4.8 17.1 1.0
CA A:TRP26 4.8 17.5 1.0
C8 A:EF3218 4.8 39.5 1.0
SG A:CYS25 4.9 22.6 1.0
O A:VAL136 4.9 16.2 1.0
CD2 A:PHE211 4.9 19.9 0.5
C9 A:EF3218 5.0 39.0 1.0
C A:ASN163 5.0 20.9 1.0

Fluorine binding site 4 out of 6 in 3n4c

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Fluorine binding site 4 out of 6 in the 6-Phenyl-1H-Imidazo[4,5-C]Pyridine-4-Carbonitrile As Cathepsin S Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of 6-Phenyl-1H-Imidazo[4,5-C]Pyridine-4-Carbonitrile As Cathepsin S Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F218

b:58.5
occ:0.75
 F23 B:EF3218 0.0 58.5 0.8
C22 B:EF3218 1.4 58.2 0.8
F25 B:EF3218 2.2 60.4 0.8
F24 B:EF3218 2.2 57.8 0.8
C6 B:EF3218 2.4 59.0 0.8
CA B:GLY137 3.0 17.8 1.0
C B:HIS164 3.2 18.5 1.0
C11 B:EF3218 3.2 58.8 0.8
O B:HIS164 3.3 17.9 1.0
N B:GLY165 3.3 17.7 1.0
C7 B:EF3218 3.3 59.4 0.8
CA B:GLY165 3.4 16.9 1.0
O17 B:EF3218 3.4 59.9 0.8
N B:HIS164 3.7 20.7 1.0
N B:GLY137 3.8 18.0 1.0
CA B:HIS164 4.0 19.2 1.0
CE B:MET71 4.0 18.8 1.0
O B:VAL136 4.1 17.9 1.0
C B:GLY137 4.2 17.7 1.0
CG2 B:VAL162 4.3 25.0 1.0
C B:VAL136 4.3 17.1 1.0
SD B:MET71 4.4 20.0 1.0
N B:VAL138 4.4 17.6 1.0
C10 B:EF3218 4.5 58.9 0.8
C B:ASN163 4.5 21.6 1.0
C8 B:EF3218 4.5 58.9 0.8
C18 B:EF3218 4.7 60.8 0.8
CB B:VAL162 4.8 23.4 1.0
C B:GLY165 4.8 16.6 1.0

Fluorine binding site 5 out of 6 in 3n4c

Go back to Fluorine Binding Sites List in 3n4c
Fluorine binding site 5 out of 6 in the 6-Phenyl-1H-Imidazo[4,5-C]Pyridine-4-Carbonitrile As Cathepsin S Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of 6-Phenyl-1H-Imidazo[4,5-C]Pyridine-4-Carbonitrile As Cathepsin S Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F218

b:57.8
occ:0.75
 F24 B:EF3218 0.0 57.8 0.8
C22 B:EF3218 1.4 58.2 0.8
F25 B:EF3218 2.2 60.4 0.8
F23 B:EF3218 2.2 58.5 0.8
C6 B:EF3218 2.4 59.0 0.8
SD B:MET71 2.7 20.0 1.0
C11 B:EF3218 2.9 58.8 0.8
CE B:MET71 3.2 18.8 1.0
CA B:GLY165 3.3 16.9 1.0
N B:GLY165 3.5 17.7 1.0
C7 B:EF3218 3.6 59.4 0.8
O17 B:EF3218 4.0 59.9 0.8
O B:GLY69 4.1 20.2 1.0
CB B:TRP26 4.1 16.6 1.0
C B:HIS164 4.2 18.5 1.0
C10 B:EF3218 4.2 58.9 0.8
CA B:TRP26 4.3 17.2 1.0
CG B:MET71 4.5 19.4 1.0
O B:HIS164 4.6 17.9 1.0
C B:GLY165 4.7 16.6 1.0
C8 B:EF3218 4.7 58.9 0.8
N B:TRP26 4.8 18.4 1.0
CA B:GLY137 4.8 17.8 1.0
O B:VAL136 4.8 17.9 1.0
SG B:CYS25 4.9 25.1 1.0
N B:MET71 4.9 19.7 1.0
N15 B:EF3218 5.0 58.7 0.8
C9 B:EF3218 5.0 58.5 0.8

Fluorine binding site 6 out of 6 in 3n4c

Go back to Fluorine Binding Sites List in 3n4c
Fluorine binding site 6 out of 6 in the 6-Phenyl-1H-Imidazo[4,5-C]Pyridine-4-Carbonitrile As Cathepsin S Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of 6-Phenyl-1H-Imidazo[4,5-C]Pyridine-4-Carbonitrile As Cathepsin S Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F218

b:60.4
occ:0.75
 F25 B:EF3218 0.0 60.4 0.8
C22 B:EF3218 1.4 58.2 0.8
F24 B:EF3218 2.2 57.8 0.8
F23 B:EF3218 2.2 58.5 0.8
O17 B:EF3218 2.4 59.9 0.8
C6 B:EF3218 2.4 59.0 0.8
C7 B:EF3218 2.8 59.4 0.8
CE B:MET71 3.5 18.8 1.0
C11 B:EF3218 3.7 58.8 0.8
C18 B:EF3218 3.7 60.8 0.8
SD B:MET71 3.9 20.0 1.0
C19 B:EF3218 4.0 59.9 0.8
C8 B:EF3218 4.2 58.9 0.8
O B:HOH309 4.3 20.0 1.0
CA B:GLY137 4.3 17.8 1.0
N B:GLY137 4.6 18.0 1.0
CG2 B:VAL162 4.6 25.0 1.0
O B:GLY69 4.8 20.2 1.0
C10 B:EF3218 4.8 58.9 0.8
CA B:GLY165 4.9 16.9 1.0

Reference:

J.Cai, M.Baugh, D.Black, C.Long, D.Jonathan Bennett, M.Dempster, X.Fradera, J.Gillespie, F.Andrews, S.Boucharens, J.Bruin, K.S.Cameron, I.Cumming, W.Hamilton, P.S.Jones, A.Kaptein, E.Kinghorn, M.Maidment, I.Martin, A.Mitchell, Z.Rankovic, J.Robinson, P.Scullion, J.C.Uitdehaag, P.Vink, P.Westwood, M.Van Zeeland, L.Van Berkom, M.Bastiani, T.Meulemans. 6-Phenyl-1H-Imidazo[4,5-C]Pyridine-4-Carbonitrile As Cathepsin S Inhibitors. Bioorg.Med.Chem.Lett. V. 20 4350 2010.
ISSN: ISSN 0960-894X
PubMed: 20598883
DOI: 10.1016/J.BMCL.2010.06.072
Page generated: Mon Jul 14 18:00:39 2025

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