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Nickel 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
Potassium (K) 1 atom
Zinc (Zn) 4 atoms
Iodine (I) 1 atom
Chlorine (Cl) 2 atoms

Nickel Binding Sites:

The binding sites of Nickel 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 Nickel atom.
In total 7 binding sites of Nickel where determined in the Novel Imidazo[1,2-A]Pyridine Derivatives with Potent Autotaxin/ENPP2 Inhibitor Activity, PDB code: 5m7m:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7;

Nickel binding site 1 out of 7 in 5m7m

Go back to Nickel Binding Sites List in 5m7m
Nickel binding site 1 out of 7 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 Nickel with other atoms in the Ni 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:Ni911

b:66.8
occ:1.00
CA A:PRO200 3.7 21.1 1.0
N A:PRO200 3.8 22.3 1.0
CG A:PRO200 4.0 21.3 1.0
CD A:PRO200 4.1 21.7 1.0
CD A:LYS500 4.1 28.6 1.0
CE A:LYS500 4.1 29.6 1.0
CB A:PRO200 4.2 21.3 1.0
CD2 A:HIS198 4.2 37.8 1.0
CG A:LYS500 4.4 27.5 1.0
C A:SER199 4.4 23.5 1.0
O A:SER199 4.8 22.4 1.0
NE2 A:HIS198 4.8 40.9 1.0
C A:PRO200 5.0 21.1 1.0

Nickel binding site 2 out of 7 in 5m7m

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Nickel binding site 2 out of 7 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 Nickel with other atoms in the Ni 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:Ni919

b:53.9
occ:1.00
CA A:TYR715 3.8 21.9 1.0
N A:TYR715 4.0 22.1 1.0
CD1 A:TYR715 4.0 22.7 1.0
C A:ASN714 4.1 23.0 1.0
O A:ASN714 4.2 23.6 1.0
CB A:TYR715 4.2 22.0 1.0
CD A:ARG718 4.3 27.1 1.0
CG2 A:VAL719 4.5 25.4 1.0
CB A:ARG718 4.5 23.6 1.0
CB A:ASN714 4.5 25.3 1.0
CG A:TYR715 4.6 22.9 1.0
NH1 A:ARG718 4.9 32.0 1.0

Nickel binding site 3 out of 7 in 5m7m

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Nickel binding site 3 out of 7 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 Nickel with other atoms in the Ni 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:Ni920

b:37.6
occ:1.00
N A:ASP783 3.4 30.1 1.0
OD1 A:ASP783 3.5 35.1 1.0
N A:ALA782 3.6 26.1 1.0
CB A:ASP783 3.8 32.4 1.0
CG A:ASP783 3.9 33.7 1.0
CB A:ALA782 3.9 27.1 1.0
CA A:ALA782 4.1 27.2 1.0
CG2 A:THR635 4.1 16.5 1.0
CA A:GLY730 4.1 14.4 1.0
CA A:ASP783 4.2 31.3 1.0
C A:ALA782 4.2 28.0 1.0
O A:VAL636 4.2 26.4 1.0
CA A:SER637 4.2 30.4 1.0
C A:PRO781 4.4 26.8 1.0
CB A:PRO781 4.4 30.6 1.0
O A:ASN729 4.5 15.3 1.0
CB A:SER637 4.7 31.4 1.0
C A:VAL636 4.8 24.3 1.0
C A:GLY730 4.8 13.5 1.0
OD2 A:ASP783 4.8 35.2 1.0
N A:SER637 4.8 27.5 1.0
CA A:PRO781 4.9 28.7 1.0
NE A:ARG595 4.9 44.8 1.0
N A:GLY730 5.0 14.8 1.0
N A:VAL731 5.0 12.3 1.0
NH2 A:ARG595 5.0 42.9 1.0

Nickel binding site 4 out of 7 in 5m7m

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Nickel binding site 4 out of 7 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 Nickel with other atoms in the Ni 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:Ni921

b:27.2
occ:1.00
N A:LEU789 3.6 21.7 1.0
NE A:ARG844 3.8 39.1 1.0
CA A:PRO788 4.1 28.2 1.0
CB A:LEU789 4.2 19.8 1.0
NH1 A:ARG844 4.3 42.8 1.0
CG A:LEU789 4.3 20.4 1.0
CB A:LEU852 4.3 20.2 1.0
CD2 A:LEU852 4.3 20.8 1.0
CD1 A:ILE849 4.3 17.9 1.0
O A:GLU848 4.4 21.9 1.0
CB A:PRO788 4.4 28.9 1.0
C A:PRO788 4.4 25.6 1.0
CA A:LEU789 4.4 19.6 1.0
CG A:ARG844 4.5 33.7 1.0
CZ A:ARG844 4.5 41.8 1.0
O A:LEU789 4.5 17.9 1.0
CD1 A:LEU852 4.6 19.9 1.0
CD A:ARG844 4.6 36.1 1.0
CG A:LEU852 4.7 20.3 1.0
C A:GLU848 4.7 21.2 1.0
CD1 A:LEU789 4.7 20.0 1.0
CB A:GLU848 4.7 23.4 1.0
CB A:ARG844 4.8 30.7 1.0
C A:LEU789 5.0 18.1 1.0

Nickel binding site 5 out of 7 in 5m7m

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Nickel binding site 5 out of 7 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 Nickel with other atoms in the Ni binding site number 5 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:Ni922

b:66.0
occ:1.00
CB A:ASP382 3.4 49.6 1.0
ND2 A:ASN400 3.6 69.3 1.0
O A:LYS402 3.7 62.4 1.0
CD1 A:TYR403 3.7 53.5 1.0
CA A:TYR403 3.8 56.4 1.0
OD2 A:ASP382 4.2 54.2 1.0
CG2 A:ILE383 4.2 36.8 1.0
C A:LYS402 4.2 61.9 1.0
CG A:ASP382 4.3 52.4 1.0
N A:TYR403 4.3 58.9 1.0
CB A:TYR403 4.3 55.4 1.0
O A:ASN379 4.4 37.1 1.0
CG A:TYR403 4.5 54.1 1.0
CG A:ASN400 4.5 66.3 1.0
CA A:ASP382 4.6 46.2 1.0
C A:ASP382 4.6 43.5 1.0
CE1 A:TYR403 4.6 51.5 1.0
OD1 A:ASN400 4.7 64.6 1.0
O A:ASP382 4.7 43.6 1.0
N A:ASP404 4.9 51.0 1.0
C A:TYR403 4.9 54.7 1.0

Nickel binding site 6 out of 7 in 5m7m

Go back to Nickel Binding Sites List in 5m7m
Nickel binding site 6 out of 7 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 Nickel with other atoms in the Ni binding site number 6 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:Ni923

b:40.6
occ:1.00
O A:PHE563 3.6 40.3 1.0
N A:LEU565 3.7 47.1 1.0
CB A:LEU565 3.8 47.9 1.0
CB A:PHE563 4.0 36.5 1.0
CG A:LEU565 4.0 47.6 1.0
C A:PHE563 4.1 41.9 1.0
N A:GLY566 4.2 53.4 1.0
CA A:LEU565 4.2 47.8 1.0
N A:CYS567 4.2 62.1 1.0
O A:CYS567 4.3 66.3 1.0
CG A:PRO655 4.3 23.6 1.0
CD1 A:LEU565 4.4 46.4 1.0
CD A:PRO655 4.5 23.6 1.0
CB A:CYS567 4.7 64.5 1.0
C A:LEU565 4.7 49.3 1.0
C A:ASP564 4.7 47.8 1.0
CA A:ASP564 4.7 47.6 1.0
CA A:PHE563 4.8 39.0 1.0
N A:ASP564 4.8 45.1 1.0
CB A:PRO655 4.8 23.8 1.0
CA A:CYS567 4.8 67.5 1.0

Nickel binding site 7 out of 7 in 5m7m

Go back to Nickel Binding Sites List in 5m7m
Nickel binding site 7 out of 7 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 Nickel with other atoms in the Ni binding site number 7 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:Ni924

b:58.7
occ:1.00
CD A:LYS710 3.4 21.4 1.0
OG A:SER677 4.0 14.6 1.0
CB A:PRO707 4.1 15.0 1.0
CB A:SER677 4.1 15.2 1.0
CG A:PRO707 4.2 15.1 1.0
CA A:PRO707 4.2 15.0 1.0
CG A:LYS710 4.3 21.0 1.0
NZ A:LYS710 4.4 23.0 1.0
CE A:LYS710 4.4 22.3 1.0
CB A:LYS710 4.8 19.9 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: Wed Dec 16 01:41:34 2020

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