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Zinc in PDB 5m7m: Novel Imidazo[1,2-A]Pyridine Derivatives with Potent Autotaxin/ENPP2 Inhibitor Activity

Enzymatic activity of Novel Imidazo[1,2-A]Pyridine Derivatives with Potent Autotaxin/ENPP2 Inhibitor Activity

All present enzymatic activity of Novel Imidazo[1,2-A]Pyridine Derivatives with Potent Autotaxin/ENPP2 Inhibitor Activity:
3.1.4.39;

Protein crystallography data

The structure of Novel Imidazo[1,2-A]Pyridine Derivatives with Potent Autotaxin/ENPP2 Inhibitor Activity, PDB code: 5m7m was solved by A.Wolhkoning, D.Fleury, P.Leonard, N.Triballeau, P.Mollat, L.Vercheval, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 78.53 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 77.450, 78.890, 78.570, 90.00, 91.87, 90.00
R / Rfree (%) 22.9 / 28.4

Other elements in 5m7m:

The structure of Novel Imidazo[1,2-A]Pyridine Derivatives with Potent Autotaxin/ENPP2 Inhibitor Activity also contains other interesting chemical elements:

Fluorine (F) 1 atom
Nickel (Ni) 7 atoms
Potassium (K) 1 atom
Iodine (I) 1 atom
Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Novel Imidazo[1,2-A]Pyridine Derivatives with Potent Autotaxin/ENPP2 Inhibitor Activity (pdb code 5m7m). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Novel Imidazo[1,2-A]Pyridine Derivatives with Potent Autotaxin/ENPP2 Inhibitor Activity, PDB code: 5m7m:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5m7m

Go back to Zinc Binding Sites List in 5m7m
Zinc binding site 1 out of 4 in the Novel Imidazo[1,2-A]Pyridine Derivatives with Potent Autotaxin/ENPP2 Inhibitor Activity


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Novel Imidazo[1,2-A]Pyridine Derivatives with Potent Autotaxin/ENPP2 Inhibitor Activity within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn915

b:20.4
occ:1.00
OD1 A:ASP312 2.0 19.0 1.0
NE2 A:HIS475 2.1 17.6 1.0
NE2 A:HIS316 2.2 22.8 1.0
O A:HOH1003 2.5 17.9 1.0
OD2 A:ASP312 2.6 20.3 1.0
CG A:ASP312 2.6 20.7 1.0
CE1 A:HIS316 3.0 23.1 1.0
O A:HOH1045 3.0 5.5 1.0
CD2 A:HIS475 3.0 17.3 1.0
CE1 A:HIS475 3.1 16.8 1.0
CD2 A:HIS316 3.3 22.9 1.0
CB A:ASP312 4.1 20.8 1.0
ND1 A:HIS475 4.2 16.3 1.0
ND1 A:HIS316 4.2 24.1 1.0
CG A:HIS475 4.2 16.8 1.0
CE1 A:HIS360 4.2 20.8 1.0
OD1 A:ASP172 4.3 25.6 1.0
CG A:HIS316 4.4 23.7 1.0
NE2 A:HIS360 4.4 21.6 1.0
OG1 A:THR210 4.5 23.1 1.0
ZN A:ZN916 4.5 28.9 1.0
CE A:MET362 4.5 21.2 1.0

Zinc binding site 2 out of 4 in 5m7m

Go back to Zinc Binding Sites List in 5m7m
Zinc binding site 2 out of 4 in the Novel Imidazo[1,2-A]Pyridine Derivatives with Potent Autotaxin/ENPP2 Inhibitor Activity


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Novel Imidazo[1,2-A]Pyridine Derivatives with Potent Autotaxin/ENPP2 Inhibitor Activity within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn916

b:28.9
occ:1.00
OD1 A:ASP172 2.0 25.6 1.0
OD2 A:ASP359 2.0 24.4 1.0
OG1 A:THR210 2.0 23.1 1.0
NE2 A:HIS360 2.1 21.6 1.0
CG A:ASP172 2.5 24.5 1.0
OD2 A:ASP172 2.5 26.8 1.0
O A:HOH1003 2.7 17.9 1.0
CD2 A:HIS360 2.9 20.3 1.0
CB A:THR210 2.9 20.3 1.0
CG A:ASP359 3.0 22.7 1.0
CE1 A:HIS360 3.1 20.8 1.0
OD1 A:ASP359 3.3 23.0 1.0
CG2 A:THR210 3.3 20.1 1.0
CA A:THR210 3.4 18.8 1.0
N A:THR210 3.8 18.2 1.0
CB A:ASP172 3.9 23.2 1.0
CG A:HIS360 4.1 19.9 1.0
ND1 A:HIS360 4.1 20.2 1.0
OD1 A:ASP312 4.3 19.0 1.0
CE1 A:HIS475 4.3 16.8 1.0
CB A:ASP359 4.3 21.5 1.0
CA A:ASP172 4.4 22.1 1.0
CG A:ASP312 4.4 20.7 1.0
ZN A:ZN915 4.5 20.4 1.0
N A:GLY173 4.5 20.9 1.0
NE2 A:HIS475 4.6 17.6 1.0
O A:HOH1045 4.7 5.5 1.0
OD2 A:ASP312 4.7 20.3 1.0
C A:LYS209 4.7 18.5 1.0
C A:ASP172 4.7 21.1 1.0
C A:THR210 4.8 17.3 1.0
CB A:ASP312 4.8 20.8 1.0
OH A:TYR307 4.9 25.7 1.0

Zinc binding site 3 out of 4 in 5m7m

Go back to Zinc Binding Sites List in 5m7m
Zinc binding site 3 out of 4 in the Novel Imidazo[1,2-A]Pyridine Derivatives with Potent Autotaxin/ENPP2 Inhibitor Activity


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Novel Imidazo[1,2-A]Pyridine Derivatives with Potent Autotaxin/ENPP2 Inhibitor Activity within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn917

b:46.6
occ:1.00
CG2 A:THR241 3.5 30.6 1.0
C A:MET233 3.7 20.9 1.0
O A:MET233 3.9 20.9 1.0
N A:MET233 4.0 20.4 1.0
CA A:MET233 4.0 21.3 1.0
N A:TYR234 4.0 20.2 1.0
CG2 A:VAL386 4.1 24.6 1.0
NH2 A:ARG394 4.1 32.2 1.0
CB A:TYR234 4.2 18.5 1.0
CB A:SER232 4.3 18.3 1.0
C A:SER232 4.5 19.5 1.0
CA A:TYR234 4.6 19.0 1.0
NH1 A:ARG394 4.6 32.3 1.0
CZ A:ARG394 4.9 32.2 1.0
CB A:THR241 4.9 29.5 1.0
CA A:SER232 4.9 18.4 1.0

Zinc binding site 4 out of 4 in 5m7m

Go back to Zinc Binding Sites List in 5m7m
Zinc binding site 4 out of 4 in the Novel Imidazo[1,2-A]Pyridine Derivatives with Potent Autotaxin/ENPP2 Inhibitor Activity


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Novel Imidazo[1,2-A]Pyridine Derivatives with Potent Autotaxin/ENPP2 Inhibitor Activity within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn918

b:33.6
occ:1.00
OD1 A:ASP744 2.0 29.3 1.0
OD1 A:ASP748 2.0 29.2 1.0
OD1 A:ASP742 2.0 26.8 1.0
O A:LEU746 2.0 25.7 1.0
OD1 A:ASP740 2.0 24.7 1.0
CG A:ASP742 3.1 24.3 1.0
CG A:ASP744 3.1 25.7 1.0
C A:LEU746 3.2 22.6 1.0
CG A:ASP740 3.3 20.7 1.0
CG A:ASP748 3.3 28.0 1.0
OD2 A:ASP742 3.4 26.5 1.0
OD2 A:ASP744 3.5 26.8 1.0
N A:LEU746 3.9 20.6 1.0
N A:ASP748 4.0 26.5 1.0
CA A:LEU746 4.0 21.7 1.0
CA A:ASP740 4.0 18.9 1.0
C A:HIS747 4.1 25.9 1.0
OD2 A:ASP748 4.1 26.8 1.0
OD2 A:ASP740 4.1 22.1 1.0
CB A:ASP740 4.1 19.3 1.0
CA A:ASP748 4.2 27.2 1.0
N A:ASP744 4.3 22.7 1.0
N A:HIS747 4.3 23.6 1.0
O A:HIS747 4.3 25.4 1.0
CB A:ASP748 4.3 28.2 1.0
CB A:ASP744 4.4 23.2 1.0
CB A:LEU746 4.4 21.8 1.0
CB A:ASP742 4.5 23.2 1.0
O A:PHE739 4.5 16.6 1.0
N A:ASP742 4.6 20.3 1.0
C A:ASP740 4.6 18.7 1.0
CA A:HIS747 4.6 25.1 1.0
N A:TYR743 4.7 21.6 1.0
CA A:ASP744 4.8 22.2 1.0
N A:GLY745 4.8 20.7 1.0
C A:ASP742 4.8 21.5 1.0
CA A:ASP742 4.8 21.7 1.0
N A:TYR741 4.9 18.4 1.0
NZ A:LYS752 4.9 31.5 1.0

Reference:

A.Joncour, N.Desroy, C.Housseman, X.Bock, N.Bienvenu, L.Cherel, V.Labeguere, C.Peixoto, D.Annoot, L.Lepissier, J.Heiermann, W.J.Hengeveld, G.Pilzak, A.Monjardet, E.Wakselman, V.Roncoroni, S.Le Tallec, R.Galien, C.David, N.Vandervoort, T.Christophe, K.Conrath, M.Jans, A.Wohlkonig, S.Soror, J.Steyaert, R.Touitou, D.Fleury, L.Vercheval, P.Mollat, N.Triballeau, E.Van Der Aar, R.Brys, B.Heckmann. Discovery, Structure-Activity Relationship, and Binding Mode of An Imidazo[1,2-A]Pyridine Series of Autotaxin Inhibitors. J. Med. Chem. V. 60 7371 2017.
ISSN: ISSN 1520-4804
PubMed: 28731719
DOI: 10.1021/ACS.JMEDCHEM.7B00647
Page generated: Sun Oct 27 21:52:09 2024

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