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Calcium in PDB 7g60: Crystal Structure of Rat Autotaxin in Complex with (2S)-6-Chloro-2- [(6-Methylsulfonyl-5,7-Dihydropyrrolo[3,4-D]Pyrimidin-2-Yl)Amino]-2, 3-Dihydro-1H-Indene-4-Carbonitrile, I.E. Smiles N(C1NC2C(CN1) Cn(S(=O)(=O)C)C2)[C@H]1CC2C(C1)C(Cc(C2)Cl)C#N with IC50=0.00218558 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with (2S)-6-Chloro-2- [(6-Methylsulfonyl-5,7-Dihydropyrrolo[3,4-D]Pyrimidin-2-Yl)Amino]-2, 3-Dihydro-1H-Indene-4-Carbonitrile, I.E. Smiles N(C1NC2C(CN1) Cn(S(=O)(=O)C)C2)[C@H]1CC2C(C1)C(Cc(C2)Cl)C#N with IC50=0.00218558 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with (2S)-6-Chloro-2- [(6-Methylsulfonyl-5,7-Dihydropyrrolo[3,4-D]Pyrimidin-2-Yl)Amino]-2, 3-Dihydro-1H-Indene-4-Carbonitrile, I.E. Smiles N(C1NC2C(CN1) Cn(S(=O)(=O)C)C2)[C@H]1CC2C(C1)C(Cc(C2)Cl)C#N with IC50=0.00218558 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with (2S)-6-Chloro-2- [(6-Methylsulfonyl-5,7-Dihydropyrrolo[3,4-D]Pyrimidin-2-Yl)Amino]-2, 3-Dihydro-1H-Indene-4-Carbonitrile, I.E. Smiles N(C1NC2C(CN1) Cn(S(=O)(=O)C)C2)[C@H]1CC2C(C1)C(Cc(C2)Cl)C#N with IC50=0.00218558 Microm, PDB code: 7g60 was solved by M.Stihle, J.Benz, D.Hunziker, E.Pinard, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 72.84 / 1.41
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.842, 91.66, 119.99, 90, 90, 90
R / Rfree (%) 16.3 / 18.8

Other elements in 7g60:

The structure of Crystal Structure of Rat Autotaxin in Complex with (2S)-6-Chloro-2- [(6-Methylsulfonyl-5,7-Dihydropyrrolo[3,4-D]Pyrimidin-2-Yl)Amino]-2, 3-Dihydro-1H-Indene-4-Carbonitrile, I.E. Smiles N(C1NC2C(CN1) Cn(S(=O)(=O)C)C2)[C@H]1CC2C(C1)C(Cc(C2)Cl)C#N with IC50=0.00218558 Microm also contains other interesting chemical elements:

Potassium (K) 1 atom
Chlorine (Cl) 1 atom
Zinc (Zn) 1 atom
Sodium (Na) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Rat Autotaxin in Complex with (2S)-6-Chloro-2- [(6-Methylsulfonyl-5,7-Dihydropyrrolo[3,4-D]Pyrimidin-2-Yl)Amino]-2, 3-Dihydro-1H-Indene-4-Carbonitrile, I.E. Smiles N(C1NC2C(CN1) Cn(S(=O)(=O)C)C2)[C@H]1CC2C(C1)C(Cc(C2)Cl)C#N with IC50=0.00218558 Microm (pdb code 7g60). 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 (2S)-6-Chloro-2- [(6-Methylsulfonyl-5,7-Dihydropyrrolo[3,4-D]Pyrimidin-2-Yl)Amino]-2, 3-Dihydro-1H-Indene-4-Carbonitrile, I.E. Smiles N(C1NC2C(CN1) Cn(S(=O)(=O)C)C2)[C@H]1CC2C(C1)C(Cc(C2)Cl)C#N with IC50=0.00218558 Microm, PDB code: 7g60:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g60

Go back to Calcium Binding Sites List in 7g60
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with (2S)-6-Chloro-2- [(6-Methylsulfonyl-5,7-Dihydropyrrolo[3,4-D]Pyrimidin-2-Yl)Amino]-2, 3-Dihydro-1H-Indene-4-Carbonitrile, I.E. Smiles N(C1NC2C(CN1) Cn(S(=O)(=O)C)C2)[C@H]1CC2C(C1)C(Cc(C2)Cl)C#N with IC50=0.00218558 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 (2S)-6-Chloro-2- [(6-Methylsulfonyl-5,7-Dihydropyrrolo[3,4-D]Pyrimidin-2-Yl)Amino]-2, 3-Dihydro-1H-Indene-4-Carbonitrile, I.E. Smiles N(C1NC2C(CN1) Cn(S(=O)(=O)C)C2)[C@H]1CC2C(C1)C(Cc(C2)Cl)C#N with IC50=0.00218558 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:16.2
occ:1.00
 OD1 A:ASP171 1.7 14.2 0.4
OG1 A:THR209 1.9 13.7 1.0
OD1 A:ASP171 1.9 15.3 0.6
NE2 A:HIS359 2.1 10.7 1.0
OD2 A:ASP358 2.2 15.6 1.0
CG A:ASP171 2.6 13.8 0.6
OD2 A:ASP171 2.8 16.1 0.6
CG A:ASP171 2.8 13.5 0.4
CE1 A:HIS359 2.9 11.0 1.0
CB A:THR209 2.9 12.2 1.0
CG A:ASP358 3.0 12.1 1.0
CD2 A:HIS359 3.0 11.7 1.0
OD1 A:ASP358 3.3 11.1 1.0
CG2 A:THR209 3.3 14.7 1.0
CA A:THR209 3.3 11.1 1.0
OD2 A:ASP171 3.4 15.4 0.4
O A:HOH1255 3.7 28.2 1.0
N A:THR209 3.9 10.5 1.0
CB A:ASP171 4.0 11.9 0.6
ND1 A:HIS359 4.0 11.7 1.0
CB A:ASP171 4.0 11.9 0.4
OD1 A:ASP311 4.0 15.8 1.0
CG A:HIS359 4.1 10.4 1.0
N A:GLY172 4.1 10.4 1.0
CA A:ASP171 4.3 11.6 0.4
CA A:ASP171 4.3 11.5 0.6
CB A:ASP358 4.3 10.4 1.0
CG A:ASP311 4.4 14.6 1.0
CE1 A:HIS474 4.4 12.3 1.0
OXT A:ACT1006 4.5 26.9 1.0
ZN A:ZN1007 4.5 13.0 1.0
O A:HOH1102 4.6 19.1 1.0
C A:ASP171 4.6 10.7 1.0
NE2 A:HIS474 4.6 10.7 1.0
C A:THR209 4.7 12.2 1.0
C A:LYS208 4.7 10.7 1.0
CB A:ASP311 4.8 11.8 1.0
OD2 A:ASP311 4.9 17.8 1.0
CA A:GLY172 5.0 10.6 1.0

Calcium binding site 2 out of 2 in 7g60

Go back to Calcium Binding Sites List in 7g60
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with (2S)-6-Chloro-2- [(6-Methylsulfonyl-5,7-Dihydropyrrolo[3,4-D]Pyrimidin-2-Yl)Amino]-2, 3-Dihydro-1H-Indene-4-Carbonitrile, I.E. Smiles N(C1NC2C(CN1) Cn(S(=O)(=O)C)C2)[C@H]1CC2C(C1)C(Cc(C2)Cl)C#N with IC50=0.00218558 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 (2S)-6-Chloro-2- [(6-Methylsulfonyl-5,7-Dihydropyrrolo[3,4-D]Pyrimidin-2-Yl)Amino]-2, 3-Dihydro-1H-Indene-4-Carbonitrile, I.E. Smiles N(C1NC2C(CN1) Cn(S(=O)(=O)C)C2)[C@H]1CC2C(C1)C(Cc(C2)Cl)C#N with IC50=0.00218558 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1009

b:10.1
occ:1.00
 OD1 A:ASP747 2.3 10.7 1.0
OD1 A:ASN741 2.3 13.0 1.0
O A:LEU745 2.3 10.5 1.0
OD1 A:ASP739 2.3 9.8 1.0
O A:HOH1702 2.3 14.8 1.0
OD1 A:ASP743 2.4 11.3 1.0
CG A:ASP743 3.3 13.9 1.0
CG A:ASN741 3.4 14.2 1.0
CG A:ASP739 3.5 9.3 1.0
C A:LEU745 3.5 10.0 1.0
CG A:ASP747 3.5 10.6 1.0
OD2 A:ASP743 3.8 15.2 1.0
ND2 A:ASN741 3.9 19.3 1.0
N A:ASP747 3.9 10.3 1.0
CA A:ASP739 3.9 8.7 1.0
C A:ARG746 4.0 11.5 1.0
N A:LEU745 4.1 9.1 1.0
CA A:ASP747 4.1 10.1 1.0
CB A:ASP739 4.2 9.3 1.0
O A:ARG746 4.2 12.0 1.0
CA A:LEU745 4.2 9.9 1.0
N A:ASP743 4.3 11.6 1.0
CB A:ASP747 4.4 9.7 1.0
OD2 A:ASP739 4.4 9.1 1.0
OD2 A:ASP747 4.4 10.5 1.0
O A:PHE738 4.4 9.6 1.0
C A:ASP739 4.5 10.3 1.0
CB A:LEU745 4.5 10.3 1.0
N A:ASN741 4.5 11.1 1.0
N A:ARG746 4.5 10.9 1.0
CB A:ASP743 4.5 12.5 1.0
OE2 A:GLU751 4.5 22.1 1.0
O A:HOH1495 4.6 22.5 1.0
CB A:ASN741 4.7 11.8 1.0
N A:TYR740 4.7 10.7 1.0
N A:TYR742 4.7 11.1 1.0
CA A:ARG746 4.8 11.3 1.0
CA A:ASP743 4.8 11.6 1.0
C A:ASN741 4.8 12.1 1.0
CA A:ASN741 4.9 11.2 1.0
N A:GLY744 4.9 9.8 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 15:53:37 2025

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