Atomistry » Calcium » PDB 7g4z-7g62 » 7g5m
Atomistry »
  Calcium »
    PDB 7g4z-7g62 »
      7g5m »

Calcium in PDB 7g5m: Crystal Structure of Rat Autotaxin in Complex with Rac-(E)-1-[Rac- (3AR,8AS)-2-(1,4,6,7-Tetrahydrotriazolo[4,5-C]Pyridine-5-Carbonyl)-1, 3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepin-6-Yl]-3-[4- (Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F)Cn(C2)C(=O) N1CCC2=C(C1)N=NN2 with IC50=0.0280543 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with Rac-(E)-1-[Rac- (3AR,8AS)-2-(1,4,6,7-Tetrahydrotriazolo[4,5-C]Pyridine-5-Carbonyl)-1, 3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepin-6-Yl]-3-[4- (Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F)Cn(C2)C(=O) N1CCC2=C(C1)N=NN2 with IC50=0.0280543 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with Rac-(E)-1-[Rac- (3AR,8AS)-2-(1,4,6,7-Tetrahydrotriazolo[4,5-C]Pyridine-5-Carbonyl)-1, 3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepin-6-Yl]-3-[4- (Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F)Cn(C2)C(=O) N1CCC2=C(C1)N=NN2 with IC50=0.0280543 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with Rac-(E)-1-[Rac- (3AR,8AS)-2-(1,4,6,7-Tetrahydrotriazolo[4,5-C]Pyridine-5-Carbonyl)-1, 3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepin-6-Yl]-3-[4- (Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F)Cn(C2)C(=O) N1CCC2=C(C1)N=NN2 with IC50=0.0280543 Microm, PDB code: 7g5m 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) 46.08 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.348, 92.166, 120.549, 90, 90, 90
R / Rfree (%) 20.1 / 24.4

Other elements in 7g5m:

The structure of Crystal Structure of Rat Autotaxin in Complex with Rac-(E)-1-[Rac- (3AR,8AS)-2-(1,4,6,7-Tetrahydrotriazolo[4,5-C]Pyridine-5-Carbonyl)-1, 3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepin-6-Yl]-3-[4- (Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F)Cn(C2)C(=O) N1CCC2=C(C1)N=NN2 with IC50=0.0280543 Microm also contains other interesting chemical elements:

Fluorine (F) 3 atoms
Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Rat Autotaxin in Complex with Rac-(E)-1-[Rac- (3AR,8AS)-2-(1,4,6,7-Tetrahydrotriazolo[4,5-C]Pyridine-5-Carbonyl)-1, 3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepin-6-Yl]-3-[4- (Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F)Cn(C2)C(=O) N1CCC2=C(C1)N=NN2 with IC50=0.0280543 Microm (pdb code 7g5m). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Crystal Structure of Rat Autotaxin in Complex with Rac-(E)-1-[Rac- (3AR,8AS)-2-(1,4,6,7-Tetrahydrotriazolo[4,5-C]Pyridine-5-Carbonyl)-1, 3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepin-6-Yl]-3-[4- (Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F)Cn(C2)C(=O) N1CCC2=C(C1)N=NN2 with IC50=0.0280543 Microm, PDB code: 7g5m:

Calcium binding site 1 out of 1 in 7g5m

Go back to Calcium Binding Sites List in 7g5m
Calcium binding site 1 out of 1 in the Crystal Structure of Rat Autotaxin in Complex with Rac-(E)-1-[Rac- (3AR,8AS)-2-(1,4,6,7-Tetrahydrotriazolo[4,5-C]Pyridine-5-Carbonyl)-1, 3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepin-6-Yl]-3-[4- (Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F)Cn(C2)C(=O) N1CCC2=C(C1)N=NN2 with IC50=0.0280543 Microm


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Rat Autotaxin in Complex with Rac-(E)-1-[Rac- (3AR,8AS)-2-(1,4,6,7-Tetrahydrotriazolo[4,5-C]Pyridine-5-Carbonyl)-1, 3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepin-6-Yl]-3-[4- (Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F)Cn(C2)C(=O) N1CCC2=C(C1)N=NN2 with IC50=0.0280543 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca905

b:35.8
occ:1.00
 OD1 A:ASP747 2.1 32.6 1.0
OD1 A:ASN741 2.2 29.5 1.0
O A:LEU745 2.2 25.9 1.0
OD1 A:ASP739 2.2 25.2 1.0
O A:HOH1262 2.3 28.1 1.0
OD1 A:ASP743 2.3 32.8 1.0
CG A:ASP743 3.2 31.6 1.0
CG A:ASN741 3.2 29.9 1.0
CG A:ASP747 3.3 36.7 1.0
C A:LEU745 3.4 23.7 1.0
CG A:ASP739 3.4 29.8 1.0
OD2 A:ASP743 3.5 34.3 1.0
ND2 A:ASN741 3.7 31.1 1.0
CA A:ASP739 3.9 28.4 1.0
N A:LEU745 4.0 22.0 1.0
C A:ARG746 4.0 28.1 1.0
N A:ASP747 4.0 28.1 1.0
OD2 A:ASP747 4.0 44.0 1.0
CB A:ASP739 4.1 28.4 1.0
CA A:LEU745 4.1 22.0 1.0
O A:ARG746 4.1 27.4 1.0
N A:ASP743 4.3 23.6 1.0
CA A:ASP747 4.3 30.0 1.0
OD2 A:ASP739 4.3 24.6 1.0
CB A:LEU745 4.3 23.8 1.0
N A:ARG746 4.4 24.1 1.0
CB A:ASP747 4.4 31.7 1.0
C A:ASP739 4.4 30.2 1.0
N A:ASN741 4.4 28.2 1.0
CB A:ASP743 4.5 25.7 1.0
O A:PHE738 4.5 25.3 1.0
CB A:ASN741 4.6 28.1 1.0
CA A:ARG746 4.6 26.9 0.5
CA A:ARG746 4.6 26.8 0.5
N A:TYR742 4.7 26.0 1.0
N A:TYR740 4.7 28.6 1.0
C A:ASN741 4.7 28.5 1.0
CA A:ASP743 4.8 25.9 1.0
CA A:ASN741 4.8 28.2 1.0
N A:GLY744 4.8 25.7 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: Sat Feb 8 15:51:36 2025

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy