Atomistry » Sodium » PDB 7f5i-7g32 » 7g2p
Atomistry »
  Sodium »
    PDB 7f5i-7g32 »
      7g2p »

Sodium 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:

Calcium (Ca) 2 atoms
Potassium (K) 1 atom
Zinc (Zn) 1 atom
Chlorine (Cl) 1 atom
Fluorine (F) 1 atom

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total only one binding site of Sodium was 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:

Sodium binding site 1 out of 1 in 7g2p

Go back to Sodium Binding Sites List in 7g2p
Sodium binding site 1 out of 1 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 Sodium with other atoms in the Na 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:Na907

b:45.1
occ:1.00
 O A:HOH1179 2.2 42.3 1.0
O A:HOH1144 2.4 40.4 1.0
OG A:SER807 2.4 35.3 1.0
O A:SER804 2.7 33.0 1.0
O A:ASN801 2.7 32.0 1.0
C A:ASN801 3.5 30.7 1.0
CB A:SER807 3.6 37.2 1.0
C A:SER804 3.7 36.1 1.0
CA A:ASP802 3.8 34.9 1.0
N A:ASP802 4.0 34.3 1.0
O A:ASP802 4.2 35.8 1.0
C A:ASP802 4.2 34.0 1.0
N A:SER807 4.2 38.6 1.0
CA A:CYS805 4.3 39.8 1.0
N A:CYS805 4.4 37.6 1.0
O A:CYS805 4.4 42.0 1.0
C A:CYS805 4.5 38.3 1.0
CA A:SER807 4.5 40.5 1.0
OD1 A:ASP802 4.5 41.7 1.0
CB A:ASN801 4.6 30.1 1.0
CA A:ASN801 4.6 31.7 1.0
N A:SER804 4.6 32.4 1.0
CA A:SER804 4.7 33.8 1.0
O A:HOH1072 4.8 48.3 1.0
O A:HOH1180 4.9 46.1 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 23:09:26 2025

Last articles

Zn in 9F7I
Zn in 9DTR
Zn in 9ESH
Zn in 9ESI
Zn in 9EMG
Zn in 9EDL
Zn in 9BZ0
Zn in 9CKF
Zn in 9CKC
Zn in 9CKG
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy