Atomistry » Fluorine » PDB 4uwg-4whq » 4w5c
Atomistry »
  Fluorine »
    PDB 4uwg-4whq »
      4w5c »

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

Go back to Fluorine Binding Sites List in 4w5c
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: Sun Dec 13 12:13:56 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy