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:
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
Go back to
Nickel Binding Sites List in 5m7m
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
Go back to
Nickel Binding Sites List in 5m7m
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
Go back to
Nickel Binding Sites List in 5m7m
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
Go back to
Nickel Binding Sites List in 5m7m
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: Thu Oct 10 06:37:11 2024
|