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Fluorine in PDB 4w5c: Crystal Structure Analysis of Cruzain with Three Fragments: 1 (N-(1H- Benzimidazol-2-Yl)-1,3-Dimethyl-Pyrazole-4-Carboxamide), 6 (2-Amino- 4,6-Difluorobenzothiazole) and 9 (N-(1H-Benzimidazol-2-Yl)-3-(4- Fluorophenyl)-1H-Pyrazole-4-Carboxamide).

Enzymatic activity of Crystal Structure Analysis of Cruzain with Three Fragments: 1 (N-(1H- Benzimidazol-2-Yl)-1,3-Dimethyl-Pyrazole-4-Carboxamide), 6 (2-Amino- 4,6-Difluorobenzothiazole) and 9 (N-(1H-Benzimidazol-2-Yl)-3-(4- Fluorophenyl)-1H-Pyrazole-4-Carboxamide).

All present enzymatic activity of Crystal Structure Analysis of Cruzain with Three Fragments: 1 (N-(1H- Benzimidazol-2-Yl)-1,3-Dimethyl-Pyrazole-4-Carboxamide), 6 (2-Amino- 4,6-Difluorobenzothiazole) and 9 (N-(1H-Benzimidazol-2-Yl)-3-(4- Fluorophenyl)-1H-Pyrazole-4-Carboxamide).:
3.4.22.51;

Protein crystallography data

The structure of Crystal Structure Analysis of Cruzain with Three Fragments: 1 (N-(1H- Benzimidazol-2-Yl)-1,3-Dimethyl-Pyrazole-4-Carboxamide), 6 (2-Amino- 4,6-Difluorobenzothiazole) and 9 (N-(1H-Benzimidazol-2-Yl)-3-(4- Fluorophenyl)-1H-Pyrazole-4-Carboxamide)., PDB code: 4w5c was solved by A.Tochowicz, J.H.Mckerrow, C.S.Craik, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.98 / 3.27
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 137.790, 137.790, 166.480, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 23.6

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure Analysis of Cruzain with Three Fragments: 1 (N-(1H- Benzimidazol-2-Yl)-1,3-Dimethyl-Pyrazole-4-Carboxamide), 6 (2-Amino- 4,6-Difluorobenzothiazole) and 9 (N-(1H-Benzimidazol-2-Yl)-3-(4- Fluorophenyl)-1H-Pyrazole-4-Carboxamide). (pdb code 4w5c). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 7 binding sites of Fluorine where determined in the Crystal Structure Analysis of Cruzain with Three Fragments: 1 (N-(1H- Benzimidazol-2-Yl)-1,3-Dimethyl-Pyrazole-4-Carboxamide), 6 (2-Amino- 4,6-Difluorobenzothiazole) and 9 (N-(1H-Benzimidazol-2-Yl)-3-(4- Fluorophenyl)-1H-Pyrazole-4-Carboxamide)., PDB code: 4w5c:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Fluorine binding site 1 out of 7 in 4w5c

Go back to Fluorine Binding Sites List in 4w5c
Fluorine binding site 1 out of 7 in the Crystal Structure Analysis of Cruzain with Three Fragments: 1 (N-(1H- Benzimidazol-2-Yl)-1,3-Dimethyl-Pyrazole-4-Carboxamide), 6 (2-Amino- 4,6-Difluorobenzothiazole) and 9 (N-(1H-Benzimidazol-2-Yl)-3-(4- Fluorophenyl)-1H-Pyrazole-4-Carboxamide).


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure Analysis of Cruzain with Three Fragments: 1 (N-(1H- Benzimidazol-2-Yl)-1,3-Dimethyl-Pyrazole-4-Carboxamide), 6 (2-Amino- 4,6-Difluorobenzothiazole) and 9 (N-(1H-Benzimidazol-2-Yl)-3-(4- Fluorophenyl)-1H-Pyrazole-4-Carboxamide). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:86.1
occ:0.80
 F22 A:3H6302 0.0 86.1 0.8
C21 A:3H6302 1.3 92.2 0.8
C20 A:3H6302 2.4 83.1 0.8
C23 A:3H6302 2.4 97.3 0.8
CB A:ALA138 3.0 64.1 1.0
C19 A:3H6302 3.6 71.3 0.8
C24 A:3H6302 3.7 0.1 0.8
CD2 A:LEU67 3.9 0.7 1.0
CD1 A:LEU160 4.0 53.3 1.0
C18 A:3H6302 4.1 89.2 0.8
CA A:ALA138 4.4 72.9 1.0
CG A:LEU67 4.4 85.1 1.0
CB A:GLU208 4.6 81.8 1.0
CG A:GLU208 4.6 93.4 1.0
CB A:LEU160 4.6 73.2 1.0
CE A:MET68 4.7 59.7 1.0
SD A:MET68 4.9 84.6 1.0
CG A:LEU160 5.0 73.6 1.0
OE1 A:GLU208 5.0 1.0 1.0

Fluorine binding site 2 out of 7 in 4w5c

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Fluorine binding site 2 out of 7 in the Crystal Structure Analysis of Cruzain with Three Fragments: 1 (N-(1H- Benzimidazol-2-Yl)-1,3-Dimethyl-Pyrazole-4-Carboxamide), 6 (2-Amino- 4,6-Difluorobenzothiazole) and 9 (N-(1H-Benzimidazol-2-Yl)-3-(4- Fluorophenyl)-1H-Pyrazole-4-Carboxamide).


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure Analysis of Cruzain with Three Fragments: 1 (N-(1H- Benzimidazol-2-Yl)-1,3-Dimethyl-Pyrazole-4-Carboxamide), 6 (2-Amino- 4,6-Difluorobenzothiazole) and 9 (N-(1H-Benzimidazol-2-Yl)-3-(4- Fluorophenyl)-1H-Pyrazole-4-Carboxamide). within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:69.7
occ:0.90
 F06 B:3H7301 0.0 69.7 0.9
C05 B:3H7301 1.3 99.9 0.9
C07 B:3H7301 2.3 0.5 0.9
C04 B:3H7301 2.4 0.9 0.9
N03 B:3H7301 3.0 0.7 0.9
O B:GLY66 3.3 0.7 1.0
C08 B:3H7301 3.6 0.8 0.9
C11 B:3H7301 3.7 0.4 0.9
CD2 B:LEU67 4.1 0.7 1.0
C10 B:3H7301 4.1 0.8 0.9
O B:ASP161 4.3 98.3 1.0
C B:HIS162 4.3 90.5 1.0
C02 B:3H7301 4.3 0.5 0.9
O B:HIS162 4.4 87.8 1.0
C B:ASP161 4.4 99.9 1.0
N B:HIS162 4.4 0.4 1.0
N B:GLY163 4.5 85.8 1.0
C B:GLY66 4.5 0.5 1.0
CA B:HIS162 4.7 94.0 1.0
F09 B:3H7301 4.7 86.7 0.9
CB B:TRP26 4.9 69.8 1.0
S12 B:3H7301 4.9 0.0 0.7
CB B:ALA138 5.0 64.8 1.0
CA B:GLY163 5.0 76.7 1.0

Fluorine binding site 3 out of 7 in 4w5c

Go back to Fluorine Binding Sites List in 4w5c
Fluorine binding site 3 out of 7 in the Crystal Structure Analysis of Cruzain with Three Fragments: 1 (N-(1H- Benzimidazol-2-Yl)-1,3-Dimethyl-Pyrazole-4-Carboxamide), 6 (2-Amino- 4,6-Difluorobenzothiazole) and 9 (N-(1H-Benzimidazol-2-Yl)-3-(4- Fluorophenyl)-1H-Pyrazole-4-Carboxamide).


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure Analysis of Cruzain with Three Fragments: 1 (N-(1H- Benzimidazol-2-Yl)-1,3-Dimethyl-Pyrazole-4-Carboxamide), 6 (2-Amino- 4,6-Difluorobenzothiazole) and 9 (N-(1H-Benzimidazol-2-Yl)-3-(4- Fluorophenyl)-1H-Pyrazole-4-Carboxamide). within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:86.7
occ:0.90
 F09 B:3H7301 0.0 86.7 0.9
C08 B:3H7301 1.3 0.8 0.9
C10 B:3H7301 2.3 0.8 0.9
C07 B:3H7301 2.4 0.5 0.9
C11 B:3H7301 3.6 0.4 0.9
C05 B:3H7301 3.6 99.9 0.9
C04 B:3H7301 4.1 0.9 0.9
O B:GLY66 4.5 0.7 1.0
F06 B:3H7301 4.7 69.7 0.9
N B:GLY66 5.0 0.5 1.0

Fluorine binding site 4 out of 7 in 4w5c

Go back to Fluorine Binding Sites List in 4w5c
Fluorine binding site 4 out of 7 in the Crystal Structure Analysis of Cruzain with Three Fragments: 1 (N-(1H- Benzimidazol-2-Yl)-1,3-Dimethyl-Pyrazole-4-Carboxamide), 6 (2-Amino- 4,6-Difluorobenzothiazole) and 9 (N-(1H-Benzimidazol-2-Yl)-3-(4- Fluorophenyl)-1H-Pyrazole-4-Carboxamide).


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure Analysis of Cruzain with Three Fragments: 1 (N-(1H- Benzimidazol-2-Yl)-1,3-Dimethyl-Pyrazole-4-Carboxamide), 6 (2-Amino- 4,6-Difluorobenzothiazole) and 9 (N-(1H-Benzimidazol-2-Yl)-3-(4- Fluorophenyl)-1H-Pyrazole-4-Carboxamide). within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F301

b:0.8
occ:0.68
 F06 C:3H7301 0.0 0.8 0.7
C05 C:3H7301 1.3 0.5 0.7
C07 C:3H7301 2.4 0.0 0.7
C04 C:3H7301 2.4 0.4 0.7
N03 C:3H7301 2.9 0.5 0.7
O C:GLY66 3.5 1.0 1.0
C11 C:3H7301 3.6 0.2 0.7
C08 C:3H7301 3.6 0.7 0.7
C10 C:3H7301 4.1 0.8 0.7
CD2 C:LEU67 4.1 0.5 1.0
C02 C:3H7301 4.2 0.4 0.7
O C:LEU160 4.3 91.0 1.0
C C:ASP161 4.3 0.5 1.0
O C:ASP161 4.4 0.5 1.0
N C:HIS162 4.6 0.1 1.0
C C:GLY66 4.7 0.1 1.0
CA C:ASP161 4.7 92.3 1.0
F09 C:3H7301 4.8 62.1 0.7
C C:HIS162 4.8 92.2 1.0
S12 C:3H7301 4.8 0.5 0.7
C C:LEU160 4.9 88.2 1.0
N C:GLY163 5.0 85.9 1.0

Fluorine binding site 5 out of 7 in 4w5c

Go back to Fluorine Binding Sites List in 4w5c
Fluorine binding site 5 out of 7 in the Crystal Structure Analysis of Cruzain with Three Fragments: 1 (N-(1H- Benzimidazol-2-Yl)-1,3-Dimethyl-Pyrazole-4-Carboxamide), 6 (2-Amino- 4,6-Difluorobenzothiazole) and 9 (N-(1H-Benzimidazol-2-Yl)-3-(4- Fluorophenyl)-1H-Pyrazole-4-Carboxamide).


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure Analysis of Cruzain with Three Fragments: 1 (N-(1H- Benzimidazol-2-Yl)-1,3-Dimethyl-Pyrazole-4-Carboxamide), 6 (2-Amino- 4,6-Difluorobenzothiazole) and 9 (N-(1H-Benzimidazol-2-Yl)-3-(4- Fluorophenyl)-1H-Pyrazole-4-Carboxamide). within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F301

b:62.1
occ:0.68
 F09 C:3H7301 0.0 62.1 0.7
C08 C:3H7301 1.3 0.7 0.7
C10 C:3H7301 2.4 0.8 0.7
C07 C:3H7301 2.4 0.0 0.7
C05 C:3H7301 3.7 0.5 0.7
C11 C:3H7301 3.7 0.2 0.7
C04 C:3H7301 4.2 0.4 0.7
O C:GLY66 4.5 1.0 1.0
F06 C:3H7301 4.8 0.8 0.7
N C:GLY66 4.9 0.0 1.0

Fluorine binding site 6 out of 7 in 4w5c

Go back to Fluorine Binding Sites List in 4w5c
Fluorine binding site 6 out of 7 in the Crystal Structure Analysis of Cruzain with Three Fragments: 1 (N-(1H- Benzimidazol-2-Yl)-1,3-Dimethyl-Pyrazole-4-Carboxamide), 6 (2-Amino- 4,6-Difluorobenzothiazole) and 9 (N-(1H-Benzimidazol-2-Yl)-3-(4- Fluorophenyl)-1H-Pyrazole-4-Carboxamide).


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure Analysis of Cruzain with Three Fragments: 1 (N-(1H- Benzimidazol-2-Yl)-1,3-Dimethyl-Pyrazole-4-Carboxamide), 6 (2-Amino- 4,6-Difluorobenzothiazole) and 9 (N-(1H-Benzimidazol-2-Yl)-3-(4- Fluorophenyl)-1H-Pyrazole-4-Carboxamide). within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F301

b:90.1
occ:0.60
 F06 D:3H7301 0.0 90.1 0.6
C05 D:3H7301 1.3 98.8 0.6
C07 D:3H7301 2.3 0.6 0.6
C04 D:3H7301 2.4 0.5 0.6
N03 D:3H7301 2.9 0.4 0.6
O D:ASP161 3.6 97.6 1.0
C08 D:3H7301 3.6 1.0 0.6
C11 D:3H7301 3.6 0.8 0.6
O D:GLY66 3.8 0.8 1.0
C D:ASP161 3.9 97.2 1.0
C10 D:3H7301 4.1 0.6 0.6
N D:HIS162 4.2 1.0 1.0
C02 D:3H7301 4.2 0.3 0.6
N D:GLY163 4.3 88.8 1.0
C D:HIS162 4.3 93.0 1.0
CA D:HIS162 4.4 99.0 1.0
CD2 D:LEU67 4.7 1.0 1.0
F09 D:3H7301 4.7 0.9 0.6
CB D:TRP26 4.7 73.2 1.0
CA D:ASP161 4.8 89.3 1.0
O D:HIS162 4.8 85.0 1.0
S12 D:3H7301 4.9 0.0 0.5
CB D:SER25 4.9 93.6 1.0
CA D:GLY163 4.9 83.4 1.0
C D:GLY66 4.9 0.1 1.0

Fluorine binding site 7 out of 7 in 4w5c

Go back to Fluorine Binding Sites List in 4w5c
Fluorine binding site 7 out of 7 in the Crystal Structure Analysis of Cruzain with Three Fragments: 1 (N-(1H- Benzimidazol-2-Yl)-1,3-Dimethyl-Pyrazole-4-Carboxamide), 6 (2-Amino- 4,6-Difluorobenzothiazole) and 9 (N-(1H-Benzimidazol-2-Yl)-3-(4- Fluorophenyl)-1H-Pyrazole-4-Carboxamide).


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure Analysis of Cruzain with Three Fragments: 1 (N-(1H- Benzimidazol-2-Yl)-1,3-Dimethyl-Pyrazole-4-Carboxamide), 6 (2-Amino- 4,6-Difluorobenzothiazole) and 9 (N-(1H-Benzimidazol-2-Yl)-3-(4- Fluorophenyl)-1H-Pyrazole-4-Carboxamide). within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F301

b:0.9
occ:0.60
 F09 D:3H7301 0.0 0.9 0.6
C08 D:3H7301 1.3 1.0 0.6
C07 D:3H7301 2.4 0.6 0.6
C10 D:3H7301 2.4 0.6 0.6
C05 D:3H7301 3.6 98.8 0.6
O D:GLY66 3.6 0.8 1.0
C11 D:3H7301 3.7 0.8 0.6
CD2 D:LEU67 4.1 1.0 1.0
N D:GLY66 4.1 0.9 1.0
C04 D:3H7301 4.1 0.5 0.6
C D:GLY66 4.3 0.1 1.0
CA D:GLY66 4.6 0.4 1.0
F06 D:3H7301 4.7 90.1 0.6
C D:GLY65 4.7 0.8 1.0
CA D:GLY65 4.8 0.7 1.0

Reference:

A.Tochowicz, G.M.Lee, M.R.Arkin, J.Neitz, J.Mckerrow, C.S.Craik. Applying Fragments Based- Drug Design to Identify Multiple Binding Modes on Cysteine Protease. To Be Published.
Page generated: Tue Jul 15 01:11:36 2025

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