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Calcium in PDB 7g2w: Crystal Structure of Rat Autotaxin in Complex with 4-[3-[(2-Tert- Butyl-4-Chloro-5-Methylphenyl)Methoxy]-4,5,7,8-Tetrahydro-1H- Pyrazolo[3,4-D]Azepine-6-Carbonyl]Benzenesulfonamide, I.E. Smiles C1(Ccc(CC1)C(=O)N1CCC2=C(CC1)Nn=C2OCC1C(Cc(C(C1)C)Cl)C(C)(C)C)S(=O) (=O)N with IC50=0.0150328 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 4-[3-[(2-Tert- Butyl-4-Chloro-5-Methylphenyl)Methoxy]-4,5,7,8-Tetrahydro-1H- Pyrazolo[3,4-D]Azepine-6-Carbonyl]Benzenesulfonamide, I.E. Smiles C1(Ccc(CC1)C(=O)N1CCC2=C(CC1)Nn=C2OCC1C(Cc(C(C1)C)Cl)C(C)(C)C)S(=O) (=O)N with IC50=0.0150328 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 4-[3-[(2-Tert- Butyl-4-Chloro-5-Methylphenyl)Methoxy]-4,5,7,8-Tetrahydro-1H- Pyrazolo[3,4-D]Azepine-6-Carbonyl]Benzenesulfonamide, I.E. Smiles C1(Ccc(CC1)C(=O)N1CCC2=C(CC1)Nn=C2OCC1C(Cc(C(C1)C)Cl)C(C)(C)C)S(=O) (=O)N with IC50=0.0150328 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 4-[3-[(2-Tert- Butyl-4-Chloro-5-Methylphenyl)Methoxy]-4,5,7,8-Tetrahydro-1H- Pyrazolo[3,4-D]Azepine-6-Carbonyl]Benzenesulfonamide, I.E. Smiles C1(Ccc(CC1)C(=O)N1CCC2=C(CC1)Nn=C2OCC1C(Cc(C(C1)C)Cl)C(C)(C)C)S(=O) (=O)N with IC50=0.0150328 Microm, PDB code: 7g2w was solved by M.Stihle, J.Benz, D.Hunziker, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.99 / 1.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 81.95, 90.58, 116.49, 90, 90, 90
R / Rfree (%) 13.2 / 16.9

Other elements in 7g2w:

The structure of Crystal Structure of Rat Autotaxin in Complex with 4-[3-[(2-Tert- Butyl-4-Chloro-5-Methylphenyl)Methoxy]-4,5,7,8-Tetrahydro-1H- Pyrazolo[3,4-D]Azepine-6-Carbonyl]Benzenesulfonamide, I.E. Smiles C1(Ccc(CC1)C(=O)N1CCC2=C(CC1)Nn=C2OCC1C(Cc(C(C1)C)Cl)C(C)(C)C)S(=O) (=O)N with IC50=0.0150328 Microm also contains other interesting chemical elements:

Potassium (K) 1 atom
Chlorine (Cl) 3 atoms
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 4-[3-[(2-Tert- Butyl-4-Chloro-5-Methylphenyl)Methoxy]-4,5,7,8-Tetrahydro-1H- Pyrazolo[3,4-D]Azepine-6-Carbonyl]Benzenesulfonamide, I.E. Smiles C1(Ccc(CC1)C(=O)N1CCC2=C(CC1)Nn=C2OCC1C(Cc(C(C1)C)Cl)C(C)(C)C)S(=O) (=O)N with IC50=0.0150328 Microm (pdb code 7g2w). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Rat Autotaxin in Complex with 4-[3-[(2-Tert- Butyl-4-Chloro-5-Methylphenyl)Methoxy]-4,5,7,8-Tetrahydro-1H- Pyrazolo[3,4-D]Azepine-6-Carbonyl]Benzenesulfonamide, I.E. Smiles C1(Ccc(CC1)C(=O)N1CCC2=C(CC1)Nn=C2OCC1C(Cc(C(C1)C)Cl)C(C)(C)C)S(=O) (=O)N with IC50=0.0150328 Microm, PDB code: 7g2w:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 7g2w

Go back to Calcium Binding Sites List in 7g2w
Calcium binding site 1 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with 4-[3-[(2-Tert- Butyl-4-Chloro-5-Methylphenyl)Methoxy]-4,5,7,8-Tetrahydro-1H- Pyrazolo[3,4-D]Azepine-6-Carbonyl]Benzenesulfonamide, I.E. Smiles C1(Ccc(CC1)C(=O)N1CCC2=C(CC1)Nn=C2OCC1C(Cc(C(C1)C)Cl)C(C)(C)C)S(=O) (=O)N with IC50=0.0150328 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-[3-[(2-Tert- Butyl-4-Chloro-5-Methylphenyl)Methoxy]-4,5,7,8-Tetrahydro-1H- Pyrazolo[3,4-D]Azepine-6-Carbonyl]Benzenesulfonamide, I.E. Smiles C1(Ccc(CC1)C(=O)N1CCC2=C(CC1)Nn=C2OCC1C(Cc(C(C1)C)Cl)C(C)(C)C)S(=O) (=O)N with IC50=0.0150328 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca903

b:26.1
occ:1.00
 O A:HOH1589 2.3 41.9 1.0
O A:HOH1761 2.3 32.6 1.0
O A:HOH1539 2.4 34.4 1.0
OD1 A:ASP72 2.4 31.7 1.0
OD2 A:ASP72 2.5 27.8 1.0
CG A:ASP72 2.8 27.0 1.0
CB A:ASP72 4.4 23.4 1.0
O A:HOH1775 4.8 40.9 1.0
O A:HOH1019 4.9 39.8 1.0
O A:HOH1537 4.9 35.5 1.0

Calcium binding site 2 out of 3 in 7g2w

Go back to Calcium Binding Sites List in 7g2w
Calcium binding site 2 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with 4-[3-[(2-Tert- Butyl-4-Chloro-5-Methylphenyl)Methoxy]-4,5,7,8-Tetrahydro-1H- Pyrazolo[3,4-D]Azepine-6-Carbonyl]Benzenesulfonamide, I.E. Smiles C1(Ccc(CC1)C(=O)N1CCC2=C(CC1)Nn=C2OCC1C(Cc(C(C1)C)Cl)C(C)(C)C)S(=O) (=O)N with IC50=0.0150328 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-[3-[(2-Tert- Butyl-4-Chloro-5-Methylphenyl)Methoxy]-4,5,7,8-Tetrahydro-1H- Pyrazolo[3,4-D]Azepine-6-Carbonyl]Benzenesulfonamide, I.E. Smiles C1(Ccc(CC1)C(=O)N1CCC2=C(CC1)Nn=C2OCC1C(Cc(C(C1)C)Cl)C(C)(C)C)S(=O) (=O)N with IC50=0.0150328 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca904

b:28.8
occ:1.00
 OG1 A:THR209 1.5 16.1 1.0
OD1 A:ASP171 2.0 14.8 1.0
NE2 A:HIS359 2.0 13.4 1.0
CG A:ASP171 2.6 13.4 1.0
OD2 A:ASP358 2.6 26.3 1.0
OD2 A:ASP171 2.6 20.4 1.0
CB A:THR209 2.7 13.3 1.0
CE1 A:HIS359 2.9 12.6 1.0
CD2 A:HIS359 3.0 11.8 1.0
CG A:ASP358 3.2 15.0 1.0
O34 A:XJC901 3.2 19.7 1.0
CA A:THR209 3.3 11.4 1.0
OD1 A:ASP358 3.3 13.9 1.0
CG2 A:THR209 3.4 15.7 1.0
N A:THR209 3.6 11.2 1.0
CB A:ASP171 3.9 12.0 1.0
O35 A:XJC901 4.0 16.9 1.0
S33 A:XJC901 4.0 18.1 1.0
ND1 A:HIS359 4.0 11.1 1.0
CG A:HIS359 4.1 11.0 1.0
OD1 A:ASP311 4.2 13.4 1.0
C6 A:XJC901 4.2 21.5 1.0
C1 A:XJC901 4.2 21.3 1.0
CA A:ASP171 4.3 11.5 1.0
N A:GLY172 4.3 10.8 1.0
CE1 A:HIS474 4.4 10.7 1.0
CB A:ASP358 4.4 13.7 1.0
CG A:ASP311 4.4 12.6 1.0
ZN A:ZN909 4.5 12.6 1.0
C A:LYS208 4.5 10.9 1.0
C A:THR209 4.7 10.5 1.0
NE2 A:HIS474 4.7 12.1 1.0
C A:ASP171 4.7 10.8 1.0
OD2 A:ASP311 4.9 14.3 1.0
CB A:ASP311 4.9 12.0 1.0

Calcium binding site 3 out of 3 in 7g2w

Go back to Calcium Binding Sites List in 7g2w
Calcium binding site 3 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with 4-[3-[(2-Tert- Butyl-4-Chloro-5-Methylphenyl)Methoxy]-4,5,7,8-Tetrahydro-1H- Pyrazolo[3,4-D]Azepine-6-Carbonyl]Benzenesulfonamide, I.E. Smiles C1(Ccc(CC1)C(=O)N1CCC2=C(CC1)Nn=C2OCC1C(Cc(C(C1)C)Cl)C(C)(C)C)S(=O) (=O)N with IC50=0.0150328 Microm


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Rat Autotaxin in Complex with 4-[3-[(2-Tert- Butyl-4-Chloro-5-Methylphenyl)Methoxy]-4,5,7,8-Tetrahydro-1H- Pyrazolo[3,4-D]Azepine-6-Carbonyl]Benzenesulfonamide, I.E. Smiles C1(Ccc(CC1)C(=O)N1CCC2=C(CC1)Nn=C2OCC1C(Cc(C(C1)C)Cl)C(C)(C)C)S(=O) (=O)N with IC50=0.0150328 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca911

b:11.3
occ:1.00
 O A:LEU745 2.3 11.3 1.0
OD1 A:ASP739 2.3 10.7 1.0
OD1 A:ASP747 2.3 12.7 1.0
OD1 A:ASN741 2.3 12.8 1.0
OD1 A:ASP743 2.3 12.6 1.0
O A:HOH1512 2.4 15.9 1.0
CG A:ASP743 3.3 13.1 1.0
CG A:ASN741 3.4 13.1 1.0
CG A:ASP739 3.5 9.9 1.0
C A:LEU745 3.5 11.2 1.0
CG A:ASP747 3.5 12.2 1.0
OD2 A:ASP743 3.8 15.6 1.0
ND2 A:ASN741 3.8 20.4 1.0
CA A:ASP739 3.9 10.4 1.0
N A:ASP747 3.9 11.3 1.0
C A:ARG746 4.0 11.7 1.0
N A:LEU745 4.1 10.8 1.0
CA A:ASP747 4.1 11.6 1.0
CB A:ASP739 4.2 10.8 1.0
CA A:LEU745 4.2 10.6 1.0
O A:ARG746 4.2 12.1 1.0
N A:ASP743 4.3 12.1 1.0
OD2 A:ASP739 4.4 11.2 1.0
OD2 A:ASP747 4.4 12.8 1.0
C A:ASP739 4.4 11.0 1.0
O A:PHE738 4.4 11.1 1.0
CB A:ASP747 4.4 12.2 1.0
CB A:LEU745 4.5 12.6 1.0
CB A:ASP743 4.5 13.1 1.0
N A:ARG746 4.5 10.8 1.0
N A:ASN741 4.5 11.5 1.0
O A:HOH1376 4.5 23.5 1.0
OE2 A:GLU751 4.6 22.0 1.0
CB A:ASN741 4.7 12.1 1.0
N A:TYR740 4.7 11.2 1.0
N A:TYR742 4.7 11.4 1.0
CA A:ARG746 4.7 10.9 1.0
CA A:ASP743 4.8 11.8 1.0
C A:ASN741 4.8 11.9 1.0
CA A:ASN741 4.8 12.0 1.0
N A:GLY744 4.9 10.9 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: Wed Jul 9 22:18:22 2025

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