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Zinc in PDB 7g5h: Crystal Structure of Rat Autotaxin in Complex with 1-[(3AR,6AR)-5-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Propan-1-One, I.E. Smiles N1(C[C@H]2[C@H](C1)Cn(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) CCC1CCC(CC1)Oc(F)(F)F with IC50=0.0098589 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 1-[(3AR,6AR)-5-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Propan-1-One, I.E. Smiles N1(C[C@H]2[C@H](C1)Cn(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) CCC1CCC(CC1)Oc(F)(F)F with IC50=0.0098589 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 1-[(3AR,6AR)-5-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Propan-1-One, I.E. Smiles N1(C[C@H]2[C@H](C1)Cn(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) CCC1CCC(CC1)Oc(F)(F)F with IC50=0.0098589 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 1-[(3AR,6AR)-5-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Propan-1-One, I.E. Smiles N1(C[C@H]2[C@H](C1)Cn(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) CCC1CCC(CC1)Oc(F)(F)F with IC50=0.0098589 Microm, PDB code: 7g5h was solved by M.Stihle, J.Benz, D.Hunziker, P.Mattei, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.39 / 2.06
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.712, 92.936, 121.168, 90, 90, 90
R / Rfree (%) 18.5 / 23.5

Other elements in 7g5h:

The structure of Crystal Structure of Rat Autotaxin in Complex with 1-[(3AR,6AR)-5-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Propan-1-One, I.E. Smiles N1(C[C@H]2[C@H](C1)Cn(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) CCC1CCC(CC1)Oc(F)(F)F with IC50=0.0098589 Microm also contains other interesting chemical elements:

Fluorine (F) 3 atoms
Calcium (Ca) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Rat Autotaxin in Complex with 1-[(3AR,6AR)-5-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Propan-1-One, I.E. Smiles N1(C[C@H]2[C@H](C1)Cn(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) CCC1CCC(CC1)Oc(F)(F)F with IC50=0.0098589 Microm (pdb code 7g5h). 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 1-[(3AR,6AR)-5-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Propan-1-One, I.E. Smiles N1(C[C@H]2[C@H](C1)Cn(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) CCC1CCC(CC1)Oc(F)(F)F with IC50=0.0098589 Microm, PDB code: 7g5h:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7g5h

Go back to Zinc Binding Sites List in 7g5h
Zinc binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 1-[(3AR,6AR)-5-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Propan-1-One, I.E. Smiles N1(C[C@H]2[C@H](C1)Cn(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) CCC1CCC(CC1)Oc(F)(F)F with IC50=0.0098589 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 1-[(3AR,6AR)-5-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Propan-1-One, I.E. Smiles N1(C[C@H]2[C@H](C1)Cn(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) CCC1CCC(CC1)Oc(F)(F)F with IC50=0.0098589 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn901

b:23.9
occ:1.00
 OG1 A:THR209 1.9 19.8 1.0
OD1 A:ASP171 2.0 21.4 1.0
OD2 A:ASP358 2.1 19.8 1.0
NE2 A:HIS359 2.2 19.4 1.0
CG A:ASP171 2.7 21.5 1.0
OD2 A:ASP171 2.8 22.4 1.0
CD2 A:HIS359 2.9 19.1 1.0
CB A:THR209 2.9 20.1 1.0
CG A:ASP358 3.0 20.7 1.0
OD1 A:ASP358 3.2 18.5 1.0
CE1 A:HIS359 3.3 20.2 1.0
CG2 A:THR209 3.3 22.1 1.0
CA A:THR209 3.4 21.2 1.0
N A:THR209 4.0 22.6 1.0
CB A:ASP171 4.0 22.4 1.0
O A:HOH1037 4.1 22.8 1.0
C15 A:YDN902 4.1 26.5 1.0
CG A:HIS359 4.1 19.1 1.0
OD2 A:ASP311 4.2 23.9 1.0
N A:GLY172 4.3 21.9 1.0
ND1 A:HIS359 4.3 19.7 1.0
CB A:ASP358 4.3 18.5 1.0
CE1 A:HIS474 4.3 26.3 1.0
CA A:ASP171 4.4 21.6 1.0
C18 A:YDN902 4.6 26.3 1.0
CG A:ASP311 4.6 22.3 1.0
N19 A:YDN902 4.6 27.0 1.0
ZN A:ZN904 4.7 24.4 1.0
NE2 A:HIS474 4.7 25.5 1.0
C A:ASP171 4.7 23.9 1.0
C A:THR209 4.7 22.4 1.0
C A:LYS208 4.8 24.8 1.0
CB A:ASP311 4.9 20.7 1.0
C14 A:YDN902 4.9 27.6 1.0

Zinc binding site 2 out of 2 in 7g5h

Go back to Zinc Binding Sites List in 7g5h
Zinc binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 1-[(3AR,6AR)-5-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Propan-1-One, I.E. Smiles N1(C[C@H]2[C@H](C1)Cn(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) CCC1CCC(CC1)Oc(F)(F)F with IC50=0.0098589 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 1-[(3AR,6AR)-5-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Propan-1-One, I.E. Smiles N1(C[C@H]2[C@H](C1)Cn(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) CCC1CCC(CC1)Oc(F)(F)F with IC50=0.0098589 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn904

b:24.4
occ:1.00
 N19 A:YDN902 1.9 27.0 1.0
OD2 A:ASP311 1.9 23.9 1.0
NE2 A:HIS474 2.0 25.5 1.0
NE2 A:HIS315 2.1 23.9 1.0
CG A:ASP311 2.6 22.3 1.0
OD1 A:ASP311 2.6 25.2 1.0
N20 A:YDN902 2.7 31.1 1.0
CD2 A:HIS474 3.0 23.7 1.0
CD2 A:HIS315 3.0 23.0 1.0
CE1 A:HIS474 3.1 26.3 1.0
C18 A:YDN902 3.1 26.3 1.0
CE1 A:HIS315 3.2 25.6 1.0
C15 A:YDN902 3.8 26.5 1.0
N21 A:YDN902 3.9 25.4 1.0
O A:HOH1037 4.0 22.8 1.0
CB A:ASP311 4.0 20.7 1.0
C17 A:YDN902 4.1 28.2 1.0
ND1 A:HIS474 4.1 22.8 1.0
CG A:HIS474 4.1 22.8 1.0
CG A:HIS315 4.2 24.2 1.0
CE1 A:HIS359 4.3 20.2 1.0
ND1 A:HIS315 4.3 25.0 1.0
NE2 A:HIS359 4.4 19.4 1.0
CE A:MET361 4.5 27.8 1.0
OG1 A:THR209 4.6 19.8 1.0
OD1 A:ASP171 4.6 21.4 1.0
ZN A:ZN901 4.7 23.9 1.0
O A:HOH1369 4.7 45.4 1.0
O A:ASP311 4.9 23.9 1.0
O A:HOH1406 5.0 48.9 1.0
CA A:ASP311 5.0 24.9 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 00:30:45 2025

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