Sodium in PDB 7jr8: 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: 7jr8 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)	32.55 / 1.13
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.082, 93.489, 47.913, 90, 105.52, 90
R / Rfree (%)	11.5 / 14.3

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
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the H-Pdgs Complexed with A 2-Phenylimidazo[1,2-A]Pyridine-6-Carboxamide Inhibitors (pdb code 7jr8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the H-Pdgs Complexed with A 2-Phenylimidazo[1,2-A]Pyridine-6-Carboxamide Inhibitors, PDB code: 7jr8:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 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 B:Na206 b:18.6 occ:1.00 O B:HOH537 2.5 18.3 0.4 O B:HOH389 2.7 11.9 1.0 OE1 B:GLN182 2.7 8.2 1.0 O B:HOH317 2.8 33.6 1.0 HB2 B:GLN182 3.1 6.3 1.0 HB3 B:GLN182 3.2 6.3 1.0 HG2 B:LYS179 3.4 14.9 0.8 O B:HOH537 3.5 21.8 0.6 HA B:LYS179 3.5 8.3 1.0 CB B:GLN182 3.6 5.2 1.0 CD B:GLN182 3.7 6.7 1.0 HZ3 B:LYS179 3.7 17.3 0.2 O B:HOH378 3.9 23.0 1.0 HZ2 B:LYS179 3.9 17.3 0.2 CG B:GLN182 4.2 5.1 1.0 HB3 B:LYS179 4.3 11.4 1.0 NZ B:LYS179 4.3 14.4 0.4 CG B:LYS179 4.3 12.4 1.0 CA B:LYS179 4.4 6.9 1.0 O B:HOH367 4.5 23.3 1.0 CB B:LYS179 4.5 9.5 1.0 HD3 B:LYS179 4.6 17.2 0.4 O B:LYS179 4.6 6.7 1.0 O B:HOH579 4.6 31.8 1.0 HG2 B:GLN182 4.7 6.1 1.0 O B:HOH560 4.7 32.5 1.0 NE2 B:GLN182 4.8 7.4 1.0 HZ1 B:LYS179 4.9 17.3 0.2 CD B:LYS179 4.9 14.3 0.7 CA B:GLN182 4.9 5.4 1.0 HG3 B:LYS179 5.0 14.9 0.7 HG3 B:GLN182 5.0 6.1 1.0 HE22 B:GLN182 5.0 8.9 1.0

Sodium binding site 2 out of 3 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 B:Na207 b:36.8 occ:1.00 O A:HOH411 2.3 38.8 1.0 O B:HOH495 2.7 14.4 1.0 O A:HOH336 3.2 12.6 1.0 O B:HOH419 3.2 21.8 1.0 HA B:ASP97 3.4 6.4 1.0 OD1 B:ASP97 3.5 7.2 1.0 HB2 B:SER100 3.6 10.9 1.0 O A:HOH430 3.6 27.4 1.0 HB2 A:SER100 3.6 14.7 1.0 HB3 A:SER100 3.7 14.7 1.0 HA A:ASP97 3.8 6.2 1.0 O A:HOH326 4.0 19.9 1.0 CB A:SER100 4.0 12.3 1.0 OD1 A:ASP97 4.0 7.1 1.0 MG B:MG204 4.0 5.7 1.0 HB3 B:SER100 4.0 10.9 1.0 OG A:SER100 4.2 15.1 1.0 CB B:SER100 4.2 9.1 1.0 CA B:ASP97 4.3 5.3 1.0 O B:HOH422 4.3 15.4 1.0 O B:HOH368 4.4 7.5 1.0 CG B:ASP97 4.5 5.9 1.0 HG A:SER100 4.5 18.1 1.0 O B:HOH544 4.6 33.6 1.0 OG B:SER100 4.6 9.5 1.0 O B:HOH546 4.6 33.1 1.0 O A:HOH362 4.7 7.6 1.0 CA A:ASP97 4.8 5.2 1.0 CB B:ASP97 4.9 5.4 1.0 O B:ASP96 4.9 5.5 1.0 N B:ASP97 4.9 4.5 1.0 HG B:SER100 5.0 11.4 1.0

Sodium binding site 3 out of 3 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 3 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 B:Na208 b:33.7 occ:1.00 O B:HOH565 2.1 27.4 1.0 O A:HOH578 2.3 23.6 1.0 O B:HOH365 2.8 25.1 1.0 O B:HOH595 2.9 32.0 1.0 HD1 B:TYR134 3.2 11.8 1.0 HA B:TYR134 3.5 8.7 1.0 CD1 B:TYR134 3.7 9.8 1.0 HE1 B:TYR134 3.9 13.1 1.0 CE1 B:TYR134 4.1 10.9 1.0 HB3 A:PRO47 4.1 13.2 1.0 O A:HOH545 4.1 34.0 1.0 O A:HOH534 4.3 35.6 1.0 O A:HOH557 4.4 30.8 1.0 CA B:TYR134 4.4 7.2 1.0 CG B:TYR134 4.5 7.4 1.0 HB2 B:TYR134 4.7 9.3 1.0 CB B:TYR134 4.8 7.7 1.0 O B:TYR134 4.8 7.4 1.0 O A:HOH395 4.8 12.2 1.0 HG22 B:THR133 4.9 14.1 1.0 CB A:PRO47 4.9 11.0 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