Atomistry » Calcium » PDB 7g4z-7g62 » 7g5d
Atomistry »
  Calcium »
    PDB 7g4z-7g62 »
      7g5d »

Calcium in PDB 7g5d: Crystal Structure of Rat Autotaxin in Complex with [(3AR,6AR)-5-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-[4-(4-Chlorophenyl)Phenyl]Methanone, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1CCC(CC1)C1CCC(CC1)Cl)C(=O) C1CCC2C(C1)N=NN2 with IC50=0.00428865 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [(3AR,6AR)-5-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-[4-(4-Chlorophenyl)Phenyl]Methanone, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1CCC(CC1)C1CCC(CC1)Cl)C(=O) C1CCC2C(C1)N=NN2 with IC50=0.00428865 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [(3AR,6AR)-5-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-[4-(4-Chlorophenyl)Phenyl]Methanone, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1CCC(CC1)C1CCC(CC1)Cl)C(=O) C1CCC2C(C1)N=NN2 with IC50=0.00428865 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with [(3AR,6AR)-5-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-[4-(4-Chlorophenyl)Phenyl]Methanone, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1CCC(CC1)C1CCC(CC1)Cl)C(=O) C1CCC2C(C1)N=NN2 with IC50=0.00428865 Microm, PDB code: 7g5d 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) 48.92 / 1.81
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.119, 91.914, 120.253, 90, 90, 90
R / Rfree (%) 18.6 / 22.5

Other elements in 7g5d:

The structure of Crystal Structure of Rat Autotaxin in Complex with [(3AR,6AR)-5-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-[4-(4-Chlorophenyl)Phenyl]Methanone, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1CCC(CC1)C1CCC(CC1)Cl)C(=O) C1CCC2C(C1)N=NN2 with IC50=0.00428865 Microm also contains other interesting chemical elements:

Sodium (Na) 2 atoms
Chlorine (Cl) 1 atom
Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Rat Autotaxin in Complex with [(3AR,6AR)-5-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-[4-(4-Chlorophenyl)Phenyl]Methanone, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1CCC(CC1)C1CCC(CC1)Cl)C(=O) C1CCC2C(C1)N=NN2 with IC50=0.00428865 Microm (pdb code 7g5d). 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 [(3AR,6AR)-5-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-[4-(4-Chlorophenyl)Phenyl]Methanone, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1CCC(CC1)C1CCC(CC1)Cl)C(=O) C1CCC2C(C1)N=NN2 with IC50=0.00428865 Microm, PDB code: 7g5d:

Calcium binding site 1 out of 1 in 7g5d

Go back to Calcium Binding Sites List in 7g5d
Calcium binding site 1 out of 1 in the Crystal Structure of Rat Autotaxin in Complex with [(3AR,6AR)-5-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-[4-(4-Chlorophenyl)Phenyl]Methanone, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1CCC(CC1)C1CCC(CC1)Cl)C(=O) C1CCC2C(C1)N=NN2 with IC50=0.00428865 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 [(3AR,6AR)-5-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-[4-(4-Chlorophenyl)Phenyl]Methanone, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1CCC(CC1)C1CCC(CC1)Cl)C(=O) C1CCC2C(C1)N=NN2 with IC50=0.00428865 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca904

b:22.4
occ:1.00
 OD1 A:ASP747 2.2 24.1 1.0
O A:HOH1364 2.3 27.9 1.0
OD1 A:ASP739 2.3 20.8 1.0
O A:LEU745 2.3 21.1 1.0
OD1 A:ASN741 2.3 26.2 1.0
OD1 A:ASP743 2.4 24.4 1.0
CG A:ASP743 3.3 24.6 1.0
CG A:ASN741 3.4 30.2 1.0
C A:LEU745 3.4 20.7 1.0
CG A:ASP739 3.5 21.7 1.0
CG A:ASP747 3.5 24.0 1.0
OD2 A:ASP743 3.7 26.2 1.0
CA A:ASP739 3.9 21.0 1.0
ND2 A:ASN741 3.9 28.8 1.0
N A:ASP747 4.0 21.1 1.0
C A:ARG746 4.0 20.2 1.0
N A:LEU745 4.1 20.2 1.0
CA A:ASP747 4.1 21.0 1.0
O A:ARG746 4.1 19.5 1.0
CB A:ASP739 4.2 21.2 1.0
CA A:LEU745 4.2 19.7 1.0
N A:ASP743 4.3 22.4 1.0
OD2 A:ASP739 4.4 21.5 1.0
C A:ASP739 4.4 22.4 1.0
OD2 A:ASP747 4.4 27.2 1.0
CB A:ASP747 4.4 21.6 1.0
CB A:LEU745 4.4 20.3 1.0
O A:PHE738 4.4 20.2 1.0
N A:ASN741 4.5 23.8 1.0
N A:ARG746 4.5 19.0 1.0
CB A:ASP743 4.5 22.5 1.0
N A:TYR740 4.6 23.3 1.0
OE2 A:GLU751 4.7 38.1 1.0
CA A:ARG746 4.7 20.1 1.0
CB A:ASN741 4.7 24.3 1.0
O A:HOH1349 4.7 35.6 1.0
N A:TYR742 4.8 21.4 1.0
CA A:ASP743 4.8 21.6 1.0
N A:GLY744 4.8 21.5 1.0
C A:ASN741 4.9 25.1 1.0
CA A:ASN741 4.9 22.9 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: Sat Feb 8 15:49:17 2025

Last articles

Zn in 8S6Z
Zn in 8S4F
Zn in 8RR4
Zn in 8RR3
Zn in 8RR1
Zn in 8RIP
Zn in 8RL5
Zn in 8RIO
Zn in 8RL9
Zn in 8RLA
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy