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Calcium in PDB 7g2p: Crystal Structure of Rat Autotaxin in Complex with 1-[2-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,4,6- Tetrahydropyrrolo[3,4-C]Pyrrole-5-Carbonyl]-4-Fluoropiperidine-4- Sulfonamide, I.E. Smiles F[C@@]1(S(=O)(=O)N)Ccn(CC1)C(=O) N1CC2=C(Cn(C(=O)C3CC(C4CC4)Nc(OCC4CCOCC4)C3)C2)C1 with IC50=0.00217681 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 1-[2-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,4,6- Tetrahydropyrrolo[3,4-C]Pyrrole-5-Carbonyl]-4-Fluoropiperidine-4- Sulfonamide, I.E. Smiles F[C@@]1(S(=O)(=O)N)Ccn(CC1)C(=O) N1CC2=C(Cn(C(=O)C3CC(C4CC4)Nc(OCC4CCOCC4)C3)C2)C1 with IC50=0.00217681 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 1-[2-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,4,6- Tetrahydropyrrolo[3,4-C]Pyrrole-5-Carbonyl]-4-Fluoropiperidine-4- Sulfonamide, I.E. Smiles F[C@@]1(S(=O)(=O)N)Ccn(CC1)C(=O) N1CC2=C(Cn(C(=O)C3CC(C4CC4)Nc(OCC4CCOCC4)C3)C2)C1 with IC50=0.00217681 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 1-[2-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,4,6- Tetrahydropyrrolo[3,4-C]Pyrrole-5-Carbonyl]-4-Fluoropiperidine-4- Sulfonamide, I.E. Smiles F[C@@]1(S(=O)(=O)N)Ccn(CC1)C(=O) N1CC2=C(Cn(C(=O)C3CC(C4CC4)Nc(OCC4CCOCC4)C3)C2)C1 with IC50=0.00217681 Microm, PDB code: 7g2p 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) 45.89 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.393, 91.776, 120.238, 90, 90, 90
R / Rfree (%) 19.2 / 23.5

Other elements in 7g2p:

The structure of Crystal Structure of Rat Autotaxin in Complex with 1-[2-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,4,6- Tetrahydropyrrolo[3,4-C]Pyrrole-5-Carbonyl]-4-Fluoropiperidine-4- Sulfonamide, I.E. Smiles F[C@@]1(S(=O)(=O)N)Ccn(CC1)C(=O) N1CC2=C(Cn(C(=O)C3CC(C4CC4)Nc(OCC4CCOCC4)C3)C2)C1 with IC50=0.00217681 Microm also contains other interesting chemical elements:

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

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Rat Autotaxin in Complex with 1-[2-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,4,6- Tetrahydropyrrolo[3,4-C]Pyrrole-5-Carbonyl]-4-Fluoropiperidine-4- Sulfonamide, I.E. Smiles F[C@@]1(S(=O)(=O)N)Ccn(CC1)C(=O) N1CC2=C(Cn(C(=O)C3CC(C4CC4)Nc(OCC4CCOCC4)C3)C2)C1 with IC50=0.00217681 Microm (pdb code 7g2p). 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 1-[2-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,4,6- Tetrahydropyrrolo[3,4-C]Pyrrole-5-Carbonyl]-4-Fluoropiperidine-4- Sulfonamide, I.E. Smiles F[C@@]1(S(=O)(=O)N)Ccn(CC1)C(=O) N1CC2=C(Cn(C(=O)C3CC(C4CC4)Nc(OCC4CCOCC4)C3)C2)C1 with IC50=0.00217681 Microm, PDB code: 7g2p:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g2p

Go back to Calcium Binding Sites List in 7g2p
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 1-[2-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,4,6- Tetrahydropyrrolo[3,4-C]Pyrrole-5-Carbonyl]-4-Fluoropiperidine-4- Sulfonamide, I.E. Smiles F[C@@]1(S(=O)(=O)N)Ccn(CC1)C(=O) N1CC2=C(Cn(C(=O)C3CC(C4CC4)Nc(OCC4CCOCC4)C3)C2)C1 with IC50=0.00217681 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 1-[2-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,4,6- Tetrahydropyrrolo[3,4-C]Pyrrole-5-Carbonyl]-4-Fluoropiperidine-4- Sulfonamide, I.E. Smiles F[C@@]1(S(=O)(=O)N)Ccn(CC1)C(=O) N1CC2=C(Cn(C(=O)C3CC(C4CC4)Nc(OCC4CCOCC4)C3)C2)C1 with IC50=0.00217681 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca901

b:52.8
occ:1.00
 OD1 A:ASP171 1.9 37.0 1.0
OG1 A:THR209 2.1 31.9 1.0
OD2 A:ASP358 2.4 26.9 1.0
NE2 A:HIS359 2.4 29.2 1.0
CG A:ASP171 2.6 32.7 1.0
OD2 A:ASP171 2.8 37.9 1.0
CE1 A:HIS359 2.9 25.7 1.0
CB A:THR209 3.0 29.4 1.0
CG2 A:THR209 3.0 31.3 1.0
CG A:ASP358 3.2 26.4 1.0
OD1 A:ASP358 3.4 23.6 1.0
CA A:THR209 3.4 29.5 1.0
O4 A:YQ0902 3.4 63.6 1.0
CD2 A:HIS359 3.5 29.0 1.0
CB A:ASP171 4.0 30.8 1.0
N A:THR209 4.0 28.5 1.0
ND1 A:HIS359 4.1 27.9 1.0
OD1 A:ASP311 4.2 30.5 1.0
N A:GLY172 4.3 26.7 1.0
CE1 A:HIS474 4.3 29.9 1.0
CA A:ASP171 4.4 27.3 1.0
CG A:ASP311 4.4 30.5 1.0
CG A:HIS359 4.4 27.1 1.0
NE2 A:HIS474 4.4 31.0 1.0
ZN A:ZN906 4.5 30.9 1.0
CB A:ASP358 4.5 24.4 1.0
C A:THR209 4.6 28.6 1.0
C A:ASP171 4.7 27.3 1.0
OD2 A:ASP311 4.8 38.2 1.0
C A:LYS208 4.8 29.9 1.0
OH A:TYR306 4.8 36.7 1.0
CB A:ASP311 4.8 31.1 1.0
O A:HOH1001 4.8 38.3 1.0
S3 A:YQ0902 4.9 62.7 1.0
O A:THR209 5.0 27.1 1.0

Calcium binding site 2 out of 2 in 7g2p

Go back to Calcium Binding Sites List in 7g2p
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 1-[2-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,4,6- Tetrahydropyrrolo[3,4-C]Pyrrole-5-Carbonyl]-4-Fluoropiperidine-4- Sulfonamide, I.E. Smiles F[C@@]1(S(=O)(=O)N)Ccn(CC1)C(=O) N1CC2=C(Cn(C(=O)C3CC(C4CC4)Nc(OCC4CCOCC4)C3)C2)C1 with IC50=0.00217681 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 1-[2-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,4,6- Tetrahydropyrrolo[3,4-C]Pyrrole-5-Carbonyl]-4-Fluoropiperidine-4- Sulfonamide, I.E. Smiles F[C@@]1(S(=O)(=O)N)Ccn(CC1)C(=O) N1CC2=C(Cn(C(=O)C3CC(C4CC4)Nc(OCC4CCOCC4)C3)C2)C1 with IC50=0.00217681 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca908

b:25.8
occ:1.00
 OD1 A:ASP747 2.3 27.0 1.0
O A:HOH1290 2.3 29.6 1.0
OD1 A:ASP743 2.3 29.0 1.0
OD1 A:ASP739 2.3 25.4 1.0
O A:LEU745 2.3 24.1 1.0
OD1 A:ASN741 2.4 29.4 1.0
CG A:ASP743 3.3 27.2 1.0
CG A:ASN741 3.4 32.2 1.0
C A:LEU745 3.5 26.2 1.0
CG A:ASP739 3.5 25.8 1.0
CG A:ASP747 3.5 27.4 1.0
OD2 A:ASP743 3.7 29.5 1.0
ND2 A:ASN741 3.7 31.8 1.0
N A:ASP747 3.9 24.4 1.0
CA A:ASP739 3.9 26.9 1.0
N A:LEU745 4.1 23.5 1.0
C A:ARG746 4.1 25.4 1.0
CA A:ASP747 4.1 26.5 1.0
CB A:ASP739 4.2 26.5 1.0
CA A:LEU745 4.2 24.7 1.0
O A:ARG746 4.3 25.3 1.0
N A:ASP743 4.3 25.7 1.0
OD2 A:ASP747 4.4 29.7 1.0
O A:PHE738 4.4 24.2 1.0
CB A:ASP747 4.4 26.0 1.0
OD2 A:ASP739 4.4 26.5 1.0
N A:ASN741 4.5 25.2 1.0
CB A:ASP743 4.5 26.3 1.0
C A:ASP739 4.5 28.4 1.0
CB A:LEU745 4.5 28.0 1.0
N A:ARG746 4.5 24.4 1.0
OE2 A:GLU751 4.6 44.5 1.0
CB A:ASN741 4.7 27.6 1.0
CA A:ARG746 4.7 25.7 1.0
CA A:ASP743 4.8 26.2 1.0
N A:TYR742 4.8 29.0 1.0
N A:TYR740 4.8 27.1 1.0
N A:GLY744 4.9 26.2 1.0
C A:ASN741 4.9 29.0 1.0
CA A:ASN741 4.9 28.4 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 15:33:32 2025

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