Atomistry » Zinc » PDB 7g3o-7g4r » 7g4i
Atomistry »
  Zinc »
    PDB 7g3o-7g4r »
      7g4i »

Zinc in PDB 7g4i: Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(3AR,6AS)-5-[2-(3,5-Dichlorophenyl)Ethylsulfonyl]-3,3A,4,5,6, 6A-Hexahydro-1H-Cyclopenta[C]Pyrrol-2-Yl]Methanone, I.E. Smiles C1(CCC2C(C1)N=NN2)C(=O)N1C[C@@H]2[C@H](C1)C[C@H](C2)S(=O)(=O) CCC1CC(Cc(C1)Cl)Cl with IC50=0.129444 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(3AR,6AS)-5-[2-(3,5-Dichlorophenyl)Ethylsulfonyl]-3,3A,4,5,6, 6A-Hexahydro-1H-Cyclopenta[C]Pyrrol-2-Yl]Methanone, I.E. Smiles C1(CCC2C(C1)N=NN2)C(=O)N1C[C@@H]2[C@H](C1)C[C@H](C2)S(=O)(=O) CCC1CC(Cc(C1)Cl)Cl with IC50=0.129444 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(3AR,6AS)-5-[2-(3,5-Dichlorophenyl)Ethylsulfonyl]-3,3A,4,5,6, 6A-Hexahydro-1H-Cyclopenta[C]Pyrrol-2-Yl]Methanone, I.E. Smiles C1(CCC2C(C1)N=NN2)C(=O)N1C[C@@H]2[C@H](C1)C[C@H](C2)S(=O)(=O) CCC1CC(Cc(C1)Cl)Cl with IC50=0.129444 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(3AR,6AS)-5-[2-(3,5-Dichlorophenyl)Ethylsulfonyl]-3,3A,4,5,6, 6A-Hexahydro-1H-Cyclopenta[C]Pyrrol-2-Yl]Methanone, I.E. Smiles C1(CCC2C(C1)N=NN2)C(=O)N1C[C@@H]2[C@H](C1)C[C@H](C2)S(=O)(=O) CCC1CC(Cc(C1)Cl)Cl with IC50=0.129444 Microm, PDB code: 7g4i was solved by M.Stihle, J.Benz, D.Hunziker, G.Tang, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.59 / 2.62
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.907, 93.091, 121.363, 90, 90, 90
R / Rfree (%) 20.6 / 27.1

Other elements in 7g4i:

The structure of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(3AR,6AS)-5-[2-(3,5-Dichlorophenyl)Ethylsulfonyl]-3,3A,4,5,6, 6A-Hexahydro-1H-Cyclopenta[C]Pyrrol-2-Yl]Methanone, I.E. Smiles C1(CCC2C(C1)N=NN2)C(=O)N1C[C@@H]2[C@H](C1)C[C@H](C2)S(=O)(=O) CCC1CC(Cc(C1)Cl)Cl with IC50=0.129444 Microm also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Calcium (Ca) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(3AR,6AS)-5-[2-(3,5-Dichlorophenyl)Ethylsulfonyl]-3,3A,4,5,6, 6A-Hexahydro-1H-Cyclopenta[C]Pyrrol-2-Yl]Methanone, I.E. Smiles C1(CCC2C(C1)N=NN2)C(=O)N1C[C@@H]2[C@H](C1)C[C@H](C2)S(=O)(=O) CCC1CC(Cc(C1)Cl)Cl with IC50=0.129444 Microm (pdb code 7g4i). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(3AR,6AS)-5-[2-(3,5-Dichlorophenyl)Ethylsulfonyl]-3,3A,4,5,6, 6A-Hexahydro-1H-Cyclopenta[C]Pyrrol-2-Yl]Methanone, I.E. Smiles C1(CCC2C(C1)N=NN2)C(=O)N1C[C@@H]2[C@H](C1)C[C@H](C2)S(=O)(=O) CCC1CC(Cc(C1)Cl)Cl with IC50=0.129444 Microm, PDB code: 7g4i:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7g4i

Go back to Zinc Binding Sites List in 7g4i
Zinc binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(3AR,6AS)-5-[2-(3,5-Dichlorophenyl)Ethylsulfonyl]-3,3A,4,5,6, 6A-Hexahydro-1H-Cyclopenta[C]Pyrrol-2-Yl]Methanone, I.E. Smiles C1(CCC2C(C1)N=NN2)C(=O)N1C[C@@H]2[C@H](C1)C[C@H](C2)S(=O)(=O) CCC1CC(Cc(C1)Cl)Cl with IC50=0.129444 Microm


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(3AR,6AS)-5-[2-(3,5-Dichlorophenyl)Ethylsulfonyl]-3,3A,4,5,6, 6A-Hexahydro-1H-Cyclopenta[C]Pyrrol-2-Yl]Methanone, I.E. Smiles C1(CCC2C(C1)N=NN2)C(=O)N1C[C@@H]2[C@H](C1)C[C@H](C2)S(=O)(=O) CCC1CC(Cc(C1)Cl)Cl with IC50=0.129444 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn901

b:43.6
occ:1.00
 OD1 A:ASP171 1.8 35.9 1.0
OD2 A:ASP358 2.0 37.3 1.0
OG1 A:THR209 2.0 35.1 1.0
NE2 A:HIS359 2.2 39.7 1.0
CG A:ASP171 2.7 36.8 1.0
CB A:THR209 2.9 37.6 1.0
CD2 A:HIS359 2.9 41.4 1.0
OD2 A:ASP171 2.9 33.7 1.0
CG A:ASP358 3.0 35.2 1.0
CG2 A:THR209 3.1 36.8 1.0
CE1 A:HIS359 3.2 41.8 1.0
OD1 A:ASP358 3.3 35.3 1.0
CA A:THR209 3.3 40.7 1.0
N A:THR209 3.8 47.9 1.0
CG A:HIS359 4.0 41.0 1.0
C03 A:Y2Q902 4.0 51.7 1.0
CB A:ASP171 4.1 33.6 1.0
ND1 A:HIS359 4.1 41.5 1.0
N A:GLY172 4.3 38.0 1.0
CB A:ASP358 4.3 34.1 1.0
OD2 A:ASP311 4.4 30.9 1.0
CA A:ASP171 4.5 35.2 1.0
CE1 A:HIS474 4.5 40.6 1.0
C A:LYS208 4.7 44.0 1.0
NE2 A:HIS474 4.7 42.1 1.0
CG A:ASP311 4.7 33.2 1.0
C A:THR209 4.7 42.8 1.0
C06 A:Y2Q902 4.7 52.4 1.0
ZN A:ZN904 4.7 36.8 1.0
C02 A:Y2Q902 4.8 49.3 1.0
C A:ASP171 4.8 37.4 1.0
N07 A:Y2Q902 4.8 54.3 1.0
CB A:ASP311 4.9 31.8 1.0

Zinc binding site 2 out of 2 in 7g4i

Go back to Zinc Binding Sites List in 7g4i
Zinc binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(3AR,6AS)-5-[2-(3,5-Dichlorophenyl)Ethylsulfonyl]-3,3A,4,5,6, 6A-Hexahydro-1H-Cyclopenta[C]Pyrrol-2-Yl]Methanone, I.E. Smiles C1(CCC2C(C1)N=NN2)C(=O)N1C[C@@H]2[C@H](C1)C[C@H](C2)S(=O)(=O) CCC1CC(Cc(C1)Cl)Cl with IC50=0.129444 Microm


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(3AR,6AS)-5-[2-(3,5-Dichlorophenyl)Ethylsulfonyl]-3,3A,4,5,6, 6A-Hexahydro-1H-Cyclopenta[C]Pyrrol-2-Yl]Methanone, I.E. Smiles C1(CCC2C(C1)N=NN2)C(=O)N1C[C@@H]2[C@H](C1)C[C@H](C2)S(=O)(=O) CCC1CC(Cc(C1)Cl)Cl with IC50=0.129444 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn904

b:36.8
occ:1.00
 N07 A:Y2Q902 1.7 54.3 1.0
OD2 A:ASP311 1.8 30.9 1.0
NE2 A:HIS315 2.1 40.1 1.0
NE2 A:HIS474 2.1 42.1 1.0
CG A:ASP311 2.5 33.2 1.0
C06 A:Y2Q902 2.6 52.4 1.0
OD1 A:ASP311 2.6 34.9 1.0
N08 A:Y2Q902 2.8 59.4 1.0
CD2 A:HIS315 3.0 40.7 1.0
CE1 A:HIS315 3.0 41.6 1.0
CD2 A:HIS474 3.1 39.9 1.0
C03 A:Y2Q902 3.1 51.7 1.0
CE1 A:HIS474 3.2 40.6 1.0
C05 A:Y2Q902 3.7 54.0 1.0
N09 A:Y2Q902 3.8 56.7 1.0
CB A:ASP311 4.0 31.8 1.0
ND1 A:HIS315 4.1 41.7 1.0
CG A:HIS315 4.1 40.2 1.0
CE1 A:HIS359 4.2 41.8 1.0
CG A:HIS474 4.2 40.6 1.0
ND1 A:HIS474 4.3 39.9 1.0
NE2 A:HIS359 4.4 39.7 1.0
C02 A:Y2Q902 4.5 49.3 1.0
OG1 A:THR209 4.5 35.1 1.0
CE A:MET361 4.6 42.4 1.0
O A:ASP311 4.6 37.3 1.0
ZN A:ZN901 4.7 43.6 1.0
OD1 A:ASP171 4.8 35.9 1.0
C04 A:Y2Q902 4.9 54.8 1.0
C A:ASP311 4.9 36.6 1.0
CA A:ASP311 4.9 33.4 1.0

Reference:

D.Hunziker, S.C.Joachim, C.Ullmer, M.G.Rudolph. Crystal Structure of A Rat Autotaxin Complex To Be Published.
Page generated: Sun Feb 9 00:26:20 2025

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy