Atomistry » Zinc » PDB 7g4s-7g5w » 7g5q
Atomistry »
  Zinc »
    PDB 7g4s-7g5w »
      7g5q »

Zinc in PDB 7g5q: Crystal Structure of Rat Autotaxin in Complex with (3S)-3-[[2-[2- Methoxy-6-[[Methyl-[(4-Methyl-1,3-Thiazol-2-Yl) Methyl]Amino]Methyl]Phenoxy]Acetyl]Amino]-N-Methyl-3-[3- (Trifluoromethyl)Phenyl]Propanamide, I.E. Smiles C1CC(Cc(C1)C(F)(F) F)[C@H](Cc(=O)Nc)Nc(=O)COC1C(CCCC1CN(CC1=Nc(=CS1)C)C)Oc with IC50=0.814833 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with (3S)-3-[[2-[2- Methoxy-6-[[Methyl-[(4-Methyl-1,3-Thiazol-2-Yl) Methyl]Amino]Methyl]Phenoxy]Acetyl]Amino]-N-Methyl-3-[3- (Trifluoromethyl)Phenyl]Propanamide, I.E. Smiles C1CC(Cc(C1)C(F)(F) F)[C@H](Cc(=O)Nc)Nc(=O)COC1C(CCCC1CN(CC1=Nc(=CS1)C)C)Oc with IC50=0.814833 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with (3S)-3-[[2-[2- Methoxy-6-[[Methyl-[(4-Methyl-1,3-Thiazol-2-Yl) Methyl]Amino]Methyl]Phenoxy]Acetyl]Amino]-N-Methyl-3-[3- (Trifluoromethyl)Phenyl]Propanamide, I.E. Smiles C1CC(Cc(C1)C(F)(F) F)[C@H](Cc(=O)Nc)Nc(=O)COC1C(CCCC1CN(CC1=Nc(=CS1)C)C)Oc with IC50=0.814833 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with (3S)-3-[[2-[2- Methoxy-6-[[Methyl-[(4-Methyl-1,3-Thiazol-2-Yl) Methyl]Amino]Methyl]Phenoxy]Acetyl]Amino]-N-Methyl-3-[3- (Trifluoromethyl)Phenyl]Propanamide, I.E. Smiles C1CC(Cc(C1)C(F)(F) F)[C@H](Cc(=O)Nc)Nc(=O)COC1C(CCCC1CN(CC1=Nc(=CS1)C)C)Oc with IC50=0.814833 Microm, PDB code: 7g5q was solved by M.Stihle, J.Benz, D.Hunziker, H.Kuhne, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.69 / 1.64
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.045, 92.177, 119.482, 90, 90, 90
R / Rfree (%) 19 / 22.4

Other elements in 7g5q:

The structure of Crystal Structure of Rat Autotaxin in Complex with (3S)-3-[[2-[2- Methoxy-6-[[Methyl-[(4-Methyl-1,3-Thiazol-2-Yl) Methyl]Amino]Methyl]Phenoxy]Acetyl]Amino]-N-Methyl-3-[3- (Trifluoromethyl)Phenyl]Propanamide, I.E. Smiles C1CC(Cc(C1)C(F)(F) F)[C@H](Cc(=O)Nc)Nc(=O)COC1C(CCCC1CN(CC1=Nc(=CS1)C)C)Oc with IC50=0.814833 Microm also contains other interesting chemical elements:

Fluorine (F) 3 atoms
Calcium (Ca) 2 atoms
Sodium (Na) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Rat Autotaxin in Complex with (3S)-3-[[2-[2- Methoxy-6-[[Methyl-[(4-Methyl-1,3-Thiazol-2-Yl) Methyl]Amino]Methyl]Phenoxy]Acetyl]Amino]-N-Methyl-3-[3- (Trifluoromethyl)Phenyl]Propanamide, I.E. Smiles C1CC(Cc(C1)C(F)(F) F)[C@H](Cc(=O)Nc)Nc(=O)COC1C(CCCC1CN(CC1=Nc(=CS1)C)C)Oc with IC50=0.814833 Microm (pdb code 7g5q). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of Rat Autotaxin in Complex with (3S)-3-[[2-[2- Methoxy-6-[[Methyl-[(4-Methyl-1,3-Thiazol-2-Yl) Methyl]Amino]Methyl]Phenoxy]Acetyl]Amino]-N-Methyl-3-[3- (Trifluoromethyl)Phenyl]Propanamide, I.E. Smiles C1CC(Cc(C1)C(F)(F) F)[C@H](Cc(=O)Nc)Nc(=O)COC1C(CCCC1CN(CC1=Nc(=CS1)C)C)Oc with IC50=0.814833 Microm, PDB code: 7g5q:

Zinc binding site 1 out of 1 in 7g5q

Go back to Zinc Binding Sites List in 7g5q
Zinc binding site 1 out of 1 in the Crystal Structure of Rat Autotaxin in Complex with (3S)-3-[[2-[2- Methoxy-6-[[Methyl-[(4-Methyl-1,3-Thiazol-2-Yl) Methyl]Amino]Methyl]Phenoxy]Acetyl]Amino]-N-Methyl-3-[3- (Trifluoromethyl)Phenyl]Propanamide, I.E. Smiles C1CC(Cc(C1)C(F)(F) F)[C@H](Cc(=O)Nc)Nc(=O)COC1C(CCCC1CN(CC1=Nc(=CS1)C)C)Oc with IC50=0.814833 Microm


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Rat Autotaxin in Complex with (3S)-3-[[2-[2- Methoxy-6-[[Methyl-[(4-Methyl-1,3-Thiazol-2-Yl) Methyl]Amino]Methyl]Phenoxy]Acetyl]Amino]-N-Methyl-3-[3- (Trifluoromethyl)Phenyl]Propanamide, I.E. Smiles C1CC(Cc(C1)C(F)(F) F)[C@H](Cc(=O)Nc)Nc(=O)COC1C(CCCC1CN(CC1=Nc(=CS1)C)C)Oc with IC50=0.814833 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn906

b:14.2
occ:1.00
 O A:HOH1497 1.8 27.2 1.0
NE2 A:HIS315 2.0 14.1 1.0
OD1 A:ASP311 2.0 15.2 1.0
NE2 A:HIS474 2.1 12.9 1.0
OD2 A:ASP311 2.5 14.5 1.0
CG A:ASP311 2.7 12.6 1.0
O A:HOH1554 2.8 26.9 1.0
CE1 A:HIS315 3.0 16.2 1.0
CD2 A:HIS315 3.0 14.8 1.0
CD2 A:HIS474 3.1 14.3 1.0
CE1 A:HIS474 3.1 16.4 1.0
OG1 A:THR209 4.1 17.5 1.0
CE1 A:HIS359 4.1 11.2 1.0
ND1 A:HIS315 4.1 15.1 1.0
CB A:ASP311 4.1 10.9 1.0
O A:HOH1032 4.1 26.8 1.0
CG A:HIS315 4.2 13.4 1.0
CG A:HIS474 4.2 13.3 1.0
ND1 A:HIS474 4.2 13.0 1.0
O A:HOH1004 4.3 27.9 1.0
NE2 A:HIS359 4.4 10.6 1.0
CA A:CA902 4.5 25.8 1.0
CE A:MET361 4.5 10.4 1.0
O A:HOH1084 4.6 30.3 1.0
OD2 A:ASP171 4.7 26.5 1.0
OD1 A:ASP171 4.8 16.6 1.0
O A:ASP311 5.0 11.6 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: Sun Feb 9 00:30:45 2025

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy