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Calcium in PDB 7g7j: Crystal Structure of Rat Autotaxin in Complex with 4-[(3AR,6AR)-2- [(E)-3-[2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Prop-2-Enoyl]-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5- Carbonyl]-3-Fluorobenzenesulfonamide, I.E. Smiles [C@@H]12CN(C(=O) C3C(Cc(CC3)S(=O)(=O)N)F)C[C@H]1CN(C2)C(=O)/C=C/C1CCC(CC1CN1N=Nc(=N1) C)C(F)(F)F with IC50=0.00194649 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 4-[(3AR,6AR)-2- [(E)-3-[2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Prop-2-Enoyl]-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5- Carbonyl]-3-Fluorobenzenesulfonamide, I.E. Smiles [C@@H]12CN(C(=O) C3C(Cc(CC3)S(=O)(=O)N)F)C[C@H]1CN(C2)C(=O)/C=C/C1CCC(CC1CN1N=Nc(=N1) C)C(F)(F)F with IC50=0.00194649 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 4-[(3AR,6AR)-2- [(E)-3-[2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Prop-2-Enoyl]-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5- Carbonyl]-3-Fluorobenzenesulfonamide, I.E. Smiles [C@@H]12CN(C(=O) C3C(Cc(CC3)S(=O)(=O)N)F)C[C@H]1CN(C2)C(=O)/C=C/C1CCC(CC1CN1N=Nc(=N1) C)C(F)(F)F with IC50=0.00194649 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 4-[(3AR,6AR)-2- [(E)-3-[2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Prop-2-Enoyl]-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5- Carbonyl]-3-Fluorobenzenesulfonamide, I.E. Smiles [C@@H]12CN(C(=O) C3C(Cc(CC3)S(=O)(=O)N)F)C[C@H]1CN(C2)C(=O)/C=C/C1CCC(CC1CN1N=Nc(=N1) C)C(F)(F)F with IC50=0.00194649 Microm, PDB code: 7g7j 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) 45.83 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.045, 91.656, 118.945, 90, 90, 90
R / Rfree (%) 18.6 / 22.8

Other elements in 7g7j:

The structure of Crystal Structure of Rat Autotaxin in Complex with 4-[(3AR,6AR)-2- [(E)-3-[2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Prop-2-Enoyl]-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5- Carbonyl]-3-Fluorobenzenesulfonamide, I.E. Smiles [C@@H]12CN(C(=O) C3C(Cc(CC3)S(=O)(=O)N)F)C[C@H]1CN(C2)C(=O)/C=C/C1CCC(CC1CN1N=Nc(=N1) C)C(F)(F)F with IC50=0.00194649 Microm also contains other interesting chemical elements:

Sodium (Na) 1 atom
Chlorine (Cl) 1 atom
Zinc (Zn) 1 atom
Potassium (K) 1 atom
Fluorine (F) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Rat Autotaxin in Complex with 4-[(3AR,6AR)-2- [(E)-3-[2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Prop-2-Enoyl]-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5- Carbonyl]-3-Fluorobenzenesulfonamide, I.E. Smiles [C@@H]12CN(C(=O) C3C(Cc(CC3)S(=O)(=O)N)F)C[C@H]1CN(C2)C(=O)/C=C/C1CCC(CC1CN1N=Nc(=N1) C)C(F)(F)F with IC50=0.00194649 Microm (pdb code 7g7j). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Rat Autotaxin in Complex with 4-[(3AR,6AR)-2- [(E)-3-[2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Prop-2-Enoyl]-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5- Carbonyl]-3-Fluorobenzenesulfonamide, I.E. Smiles [C@@H]12CN(C(=O) C3C(Cc(CC3)S(=O)(=O)N)F)C[C@H]1CN(C2)C(=O)/C=C/C1CCC(CC1CN1N=Nc(=N1) C)C(F)(F)F with IC50=0.00194649 Microm, PDB code: 7g7j:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g7j

Go back to Calcium Binding Sites List in 7g7j
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 4-[(3AR,6AR)-2- [(E)-3-[2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Prop-2-Enoyl]-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5- Carbonyl]-3-Fluorobenzenesulfonamide, I.E. Smiles [C@@H]12CN(C(=O) C3C(Cc(CC3)S(=O)(=O)N)F)C[C@H]1CN(C2)C(=O)/C=C/C1CCC(CC1CN1N=Nc(=N1) C)C(F)(F)F with IC50=0.00194649 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 4-[(3AR,6AR)-2- [(E)-3-[2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Prop-2-Enoyl]-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5- Carbonyl]-3-Fluorobenzenesulfonamide, I.E. Smiles [C@@H]12CN(C(=O) C3C(Cc(CC3)S(=O)(=O)N)F)C[C@H]1CN(C2)C(=O)/C=C/C1CCC(CC1CN1N=Nc(=N1) C)C(F)(F)F with IC50=0.00194649 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca902

b:42.2
occ:1.00
 OG1 A:THR209 1.7 26.2 1.0
OD1 A:ASP171 1.9 33.4 1.0
NE2 A:HIS359 1.9 22.0 1.0
OD2 A:ASP358 2.3 31.4 1.0
CG A:ASP171 2.7 31.4 1.0
CB A:THR209 2.9 23.7 1.0
CD2 A:HIS359 2.9 22.2 1.0
CE1 A:HIS359 2.9 22.8 1.0
OD2 A:ASP171 3.1 41.2 1.0
CG A:ASP358 3.1 28.4 1.0
O15 A:XSB901 3.1 54.0 1.0
OD1 A:ASP358 3.3 25.1 1.0
CA A:THR209 3.3 21.2 1.0
CG2 A:THR209 3.3 24.0 1.0
N A:THR209 3.8 21.3 1.0
ND1 A:HIS359 4.0 21.7 1.0
CG A:HIS359 4.0 21.2 1.0
CB A:ASP171 4.0 25.0 1.0
S13 A:XSB901 4.1 52.7 1.0
N A:GLY172 4.2 22.2 1.0
OD1 A:ASP311 4.2 23.7 1.0
CA A:ASP171 4.3 24.6 1.0
O16 A:XSB901 4.4 47.5 1.0
CE1 A:HIS474 4.4 22.8 1.0
CB A:ASP358 4.4 22.9 1.0
C9 A:XSB901 4.4 45.6 1.0
CG A:ASP311 4.5 24.4 1.0
C10 A:XSB901 4.5 51.4 1.0
ZN A:ZN906 4.6 26.8 1.0
C A:LYS208 4.6 23.7 1.0
C A:ASP171 4.6 23.3 1.0
NE2 A:HIS474 4.6 22.7 1.0
C A:THR209 4.7 21.5 1.0
OD2 A:ASP311 4.9 26.6 1.0
CB A:ASP311 4.9 23.0 1.0
CA A:GLY172 5.0 20.7 1.0

Calcium binding site 2 out of 2 in 7g7j

Go back to Calcium Binding Sites List in 7g7j
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 4-[(3AR,6AR)-2- [(E)-3-[2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Prop-2-Enoyl]-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5- Carbonyl]-3-Fluorobenzenesulfonamide, I.E. Smiles [C@@H]12CN(C(=O) C3C(Cc(CC3)S(=O)(=O)N)F)C[C@H]1CN(C2)C(=O)/C=C/C1CCC(CC1CN1N=Nc(=N1) C)C(F)(F)F with IC50=0.00194649 Microm


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Rat Autotaxin in Complex with 4-[(3AR,6AR)-2- [(E)-3-[2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Prop-2-Enoyl]-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5- Carbonyl]-3-Fluorobenzenesulfonamide, I.E. Smiles [C@@H]12CN(C(=O) C3C(Cc(CC3)S(=O)(=O)N)F)C[C@H]1CN(C2)C(=O)/C=C/C1CCC(CC1CN1N=Nc(=N1) C)C(F)(F)F with IC50=0.00194649 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca908

b:21.1
occ:1.00
 OD1 A:ASP747 2.3 24.8 1.0
O A:LEU745 2.3 19.4 1.0
OD1 A:ASP739 2.3 19.7 1.0
O A:HOH1347 2.3 28.0 1.0
OD1 A:ASP743 2.3 22.6 1.0
OD1 A:ASN741 2.3 21.6 1.0
CG A:ASP743 3.3 23.9 1.0
CG A:ASN741 3.4 26.3 1.0
CG A:ASP739 3.4 19.7 1.0
C A:LEU745 3.5 21.8 1.0
CG A:ASP747 3.5 26.0 1.0
OD2 A:ASP743 3.7 25.8 1.0
N A:ASP747 3.9 20.4 1.0
ND2 A:ASN741 3.9 27.8 1.0
CA A:ASP739 3.9 19.4 1.0
N A:LEU745 4.1 19.5 1.0
C A:ARG746 4.1 22.4 1.0
CA A:LEU745 4.2 20.8 1.0
CB A:ASP739 4.2 20.0 1.0
CA A:ASP747 4.2 22.9 1.0
O A:ARG746 4.3 20.6 1.0
N A:ASP743 4.3 20.6 1.0
OD2 A:ASP747 4.4 26.9 1.0
OD2 A:ASP739 4.4 21.0 1.0
O A:PHE738 4.4 19.8 1.0
CB A:ASP747 4.5 22.7 1.0
N A:ARG746 4.5 21.3 1.0
C A:ASP739 4.5 20.3 1.0
N A:ASN741 4.5 21.1 1.0
CB A:LEU745 4.5 24.5 1.0
CB A:ASP743 4.5 22.8 1.0
CB A:ASN741 4.7 23.9 1.0
N A:TYR740 4.7 20.4 1.0
CA A:ARG746 4.8 20.2 1.0
N A:TYR742 4.8 23.5 1.0
CA A:ASP743 4.8 22.4 1.0
N A:GLY744 4.8 23.1 1.0
C A:ASN741 4.9 24.3 1.0
O A:HOH1329 4.9 47.6 1.0
CA A:ASN741 4.9 22.9 1.0
OE2 A:GLU751 4.9 47.8 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 16:03:01 2025

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