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Potassium in PDB 4l1o: Crystal Structure of Human ALDH3A1 with Inhibitor 1-{[4-(1,3- Benzodioxol-5-Ylmethyl)Piperazin-1-Yl]Methyl}-1H-Indole-2,3-Dione

Enzymatic activity of Crystal Structure of Human ALDH3A1 with Inhibitor 1-{[4-(1,3- Benzodioxol-5-Ylmethyl)Piperazin-1-Yl]Methyl}-1H-Indole-2,3-Dione

All present enzymatic activity of Crystal Structure of Human ALDH3A1 with Inhibitor 1-{[4-(1,3- Benzodioxol-5-Ylmethyl)Piperazin-1-Yl]Methyl}-1H-Indole-2,3-Dione:
1.2.1.5;

Protein crystallography data

The structure of Crystal Structure of Human ALDH3A1 with Inhibitor 1-{[4-(1,3- Benzodioxol-5-Ylmethyl)Piperazin-1-Yl]Methyl}-1H-Indole-2,3-Dione, PDB code: 4l1o was solved by T.D.Hurley, B.Parajuli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.95 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.257, 86.396, 170.225, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 22.5

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Human ALDH3A1 with Inhibitor 1-{[4-(1,3- Benzodioxol-5-Ylmethyl)Piperazin-1-Yl]Methyl}-1H-Indole-2,3-Dione (pdb code 4l1o). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Crystal Structure of Human ALDH3A1 with Inhibitor 1-{[4-(1,3- Benzodioxol-5-Ylmethyl)Piperazin-1-Yl]Methyl}-1H-Indole-2,3-Dione, PDB code: 4l1o:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 4l1o

Go back to Potassium Binding Sites List in 4l1o
Potassium binding site 1 out of 4 in the Crystal Structure of Human ALDH3A1 with Inhibitor 1-{[4-(1,3- Benzodioxol-5-Ylmethyl)Piperazin-1-Yl]Methyl}-1H-Indole-2,3-Dione


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of Human ALDH3A1 with Inhibitor 1-{[4-(1,3- Benzodioxol-5-Ylmethyl)Piperazin-1-Yl]Methyl}-1H-Indole-2,3-Dione within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K602

b:23.7
occ:1.00
 O A:HOH715 2.6 8.6 1.0
O A:ASP322 2.9 12.3 1.0
O A:HOH821 3.0 19.4 1.0
O A:THR321 3.2 11.2 1.0
C A:ASP322 3.7 12.3 1.0
CB A:LYS301 4.2 12.5 1.0
N A:LYS301 4.2 12.9 1.0
CA A:VAL323 4.3 12.8 1.0
CB A:ASP322 4.3 12.0 1.0
N A:VAL323 4.3 12.6 1.0
C A:THR321 4.4 11.3 1.0
OE1 A:GLN300 4.4 13.8 1.0
CA A:ASP322 4.5 11.9 1.0
O A:HOH742 4.9 9.7 1.0
CA A:LYS301 4.9 12.7 1.0
N A:ASP322 4.9 11.7 1.0
N A:ASP324 4.9 13.2 1.0

Potassium binding site 2 out of 4 in 4l1o

Go back to Potassium Binding Sites List in 4l1o
Potassium binding site 2 out of 4 in the Crystal Structure of Human ALDH3A1 with Inhibitor 1-{[4-(1,3- Benzodioxol-5-Ylmethyl)Piperazin-1-Yl]Methyl}-1H-Indole-2,3-Dione


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of Human ALDH3A1 with Inhibitor 1-{[4-(1,3- Benzodioxol-5-Ylmethyl)Piperazin-1-Yl]Methyl}-1H-Indole-2,3-Dione within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K603

b:48.8
occ:1.00
 O A:TYR442 3.0 26.1 1.0
O A:LYS439 3.0 33.4 1.0
O A:PRO444 3.7 29.2 1.0
C A:TYR442 3.9 26.1 1.0
C A:LYS439 4.2 33.5 1.0
O A:HOH977 4.4 29.8 1.0
O A:PRO443 4.4 26.8 1.0
CB A:TYR442 4.4 25.7 1.0
C A:PRO443 4.4 27.1 1.0
O A:VAL440 4.5 30.6 1.0
CA A:TYR442 4.5 26.0 1.0
N A:TYR442 4.6 26.1 1.0
CA A:VAL440 4.6 31.8 1.0
N A:PRO444 4.6 28.0 1.0
C A:VAL440 4.7 30.5 1.0
C A:PRO444 4.7 29.4 1.0
CD A:PRO444 4.8 27.9 1.0
N A:VAL440 4.8 32.6 1.0
N A:PRO443 4.9 26.1 1.0
O A:HOH864 4.9 28.3 1.0
CA A:PRO443 5.0 26.6 1.0

Potassium binding site 3 out of 4 in 4l1o

Go back to Potassium Binding Sites List in 4l1o
Potassium binding site 3 out of 4 in the Crystal Structure of Human ALDH3A1 with Inhibitor 1-{[4-(1,3- Benzodioxol-5-Ylmethyl)Piperazin-1-Yl]Methyl}-1H-Indole-2,3-Dione


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of Human ALDH3A1 with Inhibitor 1-{[4-(1,3- Benzodioxol-5-Ylmethyl)Piperazin-1-Yl]Methyl}-1H-Indole-2,3-Dione within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K602

b:42.0
occ:1.00
 O B:HOH991 2.8 41.0 1.0
O B:GLU79 2.8 19.3 1.0
O B:HOH893 2.9 22.4 1.0
O B:ALA82 3.0 15.4 1.0
O B:TRP80 3.3 18.1 1.0
C B:TRP80 3.8 17.8 1.0
C B:GLU79 3.9 19.5 1.0
CA B:TRP80 4.0 18.4 1.0
O B:HOH848 4.0 21.5 1.0
C B:ALA82 4.0 15.8 1.0
O B:HOH734 4.1 13.5 1.0
CB B:GLU84 4.1 18.6 1.0
N B:ALA82 4.2 16.0 1.0
OE1 B:GLU84 4.3 20.6 1.0
N B:TRP80 4.4 18.9 1.0
CA B:ALA82 4.4 16.0 1.0
CB B:ALA82 4.5 15.9 1.0
CG B:GLU84 4.6 19.2 1.0
N B:ALA81 4.7 17.3 1.0
CA B:GLU84 4.7 17.9 1.0
N B:GLU84 4.7 17.2 1.0
C B:ASP83 4.8 16.8 1.0
O B:ASP83 4.8 16.7 1.0
C B:ALA81 4.8 16.2 1.0
CD B:GLU84 4.9 19.9 1.0

Potassium binding site 4 out of 4 in 4l1o

Go back to Potassium Binding Sites List in 4l1o
Potassium binding site 4 out of 4 in the Crystal Structure of Human ALDH3A1 with Inhibitor 1-{[4-(1,3- Benzodioxol-5-Ylmethyl)Piperazin-1-Yl]Methyl}-1H-Indole-2,3-Dione


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of Human ALDH3A1 with Inhibitor 1-{[4-(1,3- Benzodioxol-5-Ylmethyl)Piperazin-1-Yl]Methyl}-1H-Indole-2,3-Dione within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K603

b:33.2
occ:1.00
 O B:HOH829 2.6 23.3 1.0
O B:LYS439 2.7 19.7 1.0
O B:HOH854 2.7 24.7 1.0
O B:TYR442 2.9 15.6 1.0
C B:LYS439 3.9 20.2 1.0
C B:TYR442 3.9 15.8 1.0
O B:PRO444 3.9 17.0 1.0
O B:VAL440 4.2 17.7 1.0
N B:TYR442 4.3 15.6 1.0
C B:VAL440 4.3 17.9 1.0
CA B:VAL440 4.4 18.8 1.0
CA B:TYR442 4.4 15.8 1.0
CB B:TYR442 4.4 15.8 1.0
O B:HOH800 4.5 22.2 1.0
O B:HOH716 4.5 18.4 1.0
N B:VAL440 4.5 19.6 1.0
O B:PRO443 4.7 15.8 1.0
C B:PRO443 4.8 15.9 1.0
CA B:LYS439 4.9 21.1 1.0
C B:PRO444 5.0 16.7 1.0
N B:PRO443 5.0 15.8 1.0

Reference:

B.Parajuli, A.Kimble-Hill, C.H.Chen, D.Mochly-Rosen, T.D.Hurley. Discovery of Indole-2,3-Diones As Novel Class of Inhibitors For Aldh Isozymes. To Be Published.
Page generated: Sun Dec 13 23:39:51 2020

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