Sodium in PDB 7jr6: H-Pdgs Complexed with A 2-Phenylimidazo[1,2-A]Pyridine-6-Carboxamide Inhibitors

All present enzymatic activity of H-Pdgs Complexed with A 2-Phenylimidazo[1,2-A]Pyridine-6-Carboxamide Inhibitors:
2.5.1.18; 5.3.99.2;

The structure of H-Pdgs Complexed with A 2-Phenylimidazo[1,2-A]Pyridine-6-Carboxamide Inhibitors, PDB code: 7jr6 was solved by R.T.Nolte, D.O.Somers, R.T.Gampe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.57 / 1.88
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	48.872, 67.997, 69.096, 90, 96.83, 90
R / Rfree (%)	17.6 / 22.3

The structure of H-Pdgs Complexed with A 2-Phenylimidazo[1,2-A]Pyridine-6-Carboxamide Inhibitors also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Fluorine	(F)	2 atoms

The binding sites of Sodium atom in the H-Pdgs Complexed with A 2-Phenylimidazo[1,2-A]Pyridine-6-Carboxamide Inhibitors (pdb code 7jr6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the H-Pdgs Complexed with A 2-Phenylimidazo[1,2-A]Pyridine-6-Carboxamide Inhibitors, PDB code: 7jr6:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the H-Pdgs Complexed with A 2-Phenylimidazo[1,2-A]Pyridine-6-Carboxamide Inhibitors


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of H-Pdgs Complexed with A 2-Phenylimidazo[1,2-A]Pyridine-6-Carboxamide Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ A:Na204 b:39.1 occ:1.00 OG A:SER145 2.4 38.1 1.0 O A:ASP76 2.6 38.5 1.0 HG22 A:THR147 2.6 26.0 1.0 O A:HOH320 2.8 39.7 1.0 O A:VAL146 2.8 22.2 1.0 O A:HOH370 3.1 24.3 1.0 HD22 A:ASN80 3.2 40.7 1.0 HB2 A:SER145 3.3 42.2 1.0 HG23 A:THR147 3.3 26.0 1.0 CB A:SER145 3.4 35.1 1.0 CG2 A:THR147 3.4 21.6 1.0 O A:SER145 3.4 26.2 1.0 C A:SER145 3.5 24.4 1.0 C A:VAL146 3.6 22.6 1.0 C A:ASP76 3.8 35.0 1.0 HA2 A:GLY79 3.8 32.8 1.0 ND2 A:ASN80 3.9 33.9 1.0 H A:GLY79 3.9 25.3 1.0 HG21 A:THR147 3.9 26.0 1.0 CA A:SER145 4.0 32.0 1.0 HA A:LEU77 4.0 26.9 1.0 HB2 A:ASP76 4.0 64.3 1.0 HA A:THR147 4.0 26.7 1.0 N A:VAL146 4.0 23.2 1.0 OD1 A:ASN80 4.1 56.0 1.0 H A:SER145 4.1 40.9 1.0 HB3 A:SER145 4.2 42.2 1.0 N A:THR147 4.3 18.6 1.0 CG A:ASN80 4.3 44.8 1.0 HD21 A:ASN80 4.4 40.7 1.0 N A:SER145 4.5 34.1 1.0 H A:VAL146 4.5 27.9 1.0 O A:HOH302 4.5 33.5 1.0 CA A:THR147 4.5 22.2 1.0 N A:GLY79 4.5 21.3 1.0 CA A:VAL146 4.5 24.7 1.0 CB A:THR147 4.5 18.3 1.0 HA A:ASP76 4.6 44.6 1.0 CA A:GLY79 4.6 27.3 1.0 CA A:LEU77 4.7 22.4 1.0 CA A:ASP76 4.7 37.1 1.0 N A:LEU77 4.7 26.0 1.0 CB A:ASP76 4.8 53.5 1.0 H A:ASN80 4.8 34.9 1.0 HA A:SER145 4.8 38.4 1.0 C A:LEU77 4.8 20.7 1.0 HB A:THR147 4.9 22.0 1.0 H A:THR147 5.0 22.3 1.0 HA A:VAL146 5.0 29.7 1.0

Sodium binding site 2 out of 2 in the H-Pdgs Complexed with A 2-Phenylimidazo[1,2-A]Pyridine-6-Carboxamide Inhibitors


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of H-Pdgs Complexed with A 2-Phenylimidazo[1,2-A]Pyridine-6-Carboxamide Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ A:Na205 b:53.3 occ:1.00 O A:HOH335 2.6 42.5 1.0 O A:ASP166 2.7 43.7 1.0 HB2 A:ASP169 2.9 54.5 1.0 O A:HOH391 2.9 42.7 1.0 OD1 A:ASN170 3.3 56.0 1.0 HZ1 A:LYS164 3.7 77.2 1.0 HB2 A:ASP166 3.7 56.8 1.0 H A:ASP169 3.7 47.3 1.0 C A:ASP166 3.9 41.5 1.0 CB A:ASP169 3.9 45.7 1.0 HZ3 A:LYS164 4.0 77.2 1.0 CG A:ASP166 4.1 57.5 1.0 OD2 A:ASP166 4.1 52.0 1.0 H A:ASN170 4.1 56.8 1.0 NZ A:LYS164 4.2 64.3 1.0 HA A:LEU167 4.3 50.0 1.0 HB3 A:ASP169 4.3 54.5 1.0 CB A:ASP166 4.3 47.5 1.0 O A:LEU167 4.3 36.9 1.0 N A:ASP169 4.4 39.6 1.0 HZ2 A:LYS164 4.4 77.2 1.0 OD1 A:ASP166 4.4 51.7 1.0 CG A:ASN170 4.5 57.5 1.0 O A:HOH415 4.5 37.2 1.0 C A:LEU167 4.5 38.5 1.0 CG A:ASP169 4.6 46.2 1.0 CA A:ASP169 4.7 42.4 1.0 N A:ASN170 4.7 47.3 1.0 OD2 A:ASP169 4.7 59.3 1.0 CA A:ASP166 4.7 46.7 1.0 HB2 A:ASN170 4.7 69.1 1.0 CA A:LEU167 4.7 41.6 1.0 N A:LEU167 4.8 38.5 1.0

D.N.Deaton, E.Diaz, Y.Do, R.T.Gampe, J.H.Guss, A.P.Hancock, H.Hobbs, S.T.Hodgson, J.Holt, M.R.Jeune, K.M.Kahler, H.F.Kramer, J.Le, P.N.Mortenson, C.Musetti, R.T.Nolte, L.A.Orband-Miller, G.E.Peckham, K.G.Petrov, B.L.Pietrak, C.Poole, D.J.Price, G.Saxty, C.A.Schulte, A.Shillings, T.L.Smalley Jr., D.O.Somers, E.L.Stewart, J.D.Stuart, S.A.Thomson. A Knowledge-Based, Structural-Aided Discovery of A Novel Class of 2-Phenylimidazo[1,2-A]Pyridine-6-Carboxamide H-Pgds Inhibitors. Bioorg.Med.Chem.Lett. 28113 2021.
ISSN: ESSN 1464-3405
PubMed: 33991628
DOI: 10.1016/J.BMCL.2021.128113