Sodium in PDB 6d9x: Discovery of Potent 2-Aryl-6,7-Dihydro-5HPYRROLO[ 1,2-A]Imidazoles As WDR5 Win-Site Inhibitors Using Fragment-Based Methods and Structure- Based Design

The structure of Discovery of Potent 2-Aryl-6,7-Dihydro-5HPYRROLO[ 1,2-A]Imidazoles As WDR5 Win-Site Inhibitors Using Fragment-Based Methods and Structure- Based Design, PDB code: 6d9x was solved by J.Phan, S.W.Fesik, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.44 / 1.83
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	81.291, 86.273, 40.288, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 24.1

The binding sites of Sodium atom in the Discovery of Potent 2-Aryl-6,7-Dihydro-5HPYRROLO[ 1,2-A]Imidazoles As WDR5 Win-Site Inhibitors Using Fragment-Based Methods and Structure- Based Design (pdb code 6d9x). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Discovery of Potent 2-Aryl-6,7-Dihydro-5HPYRROLO[ 1,2-A]Imidazoles As WDR5 Win-Site Inhibitors Using Fragment-Based Methods and Structure- Based Design, PDB code: 6d9x:

Sodium binding site 1 out of 1 in the Discovery of Potent 2-Aryl-6,7-Dihydro-5HPYRROLO[ 1,2-A]Imidazoles As WDR5 Win-Site Inhibitors Using Fragment-Based Methods and Structure- Based Design


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Discovery of Potent 2-Aryl-6,7-Dihydro-5HPYRROLO[ 1,2-A]Imidazoles As WDR5 Win-Site Inhibitors Using Fragment-Based Methods and Structure- Based Design within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:42.3 occ:1.00 OG A:SER218 2.6 37.9 1.0 OD1 A:ASN257 2.8 47.5 1.0 N A:ILE262 2.8 38.5 1.0 O A:ILE262 3.0 34.0 1.0 CB A:SER218 3.3 39.1 1.0 CB A:ALA232 3.4 37.7 1.0 CA A:ILE262 3.5 35.6 1.0 CB A:ILE262 3.6 34.8 1.0 O A:TYR260 3.6 34.4 1.0 C A:ILE262 3.7 37.4 1.0 CG A:ASN257 3.8 42.1 1.0 C A:CYS261 3.8 36.1 1.0 CA A:CYS261 3.9 33.8 1.0 ND2 A:ASN257 4.1 42.3 1.0 C A:SER218 4.1 38.4 1.0 CB A:PHE219 4.1 32.5 1.0 O A:SER218 4.3 39.6 1.0 CG1 A:ILE262 4.3 39.1 1.0 CA A:SER218 4.3 37.4 1.0 N A:PHE219 4.4 35.9 1.0 O A:HOH646 4.5 48.5 1.0 C A:TYR260 4.5 33.1 1.0 N A:CYS261 4.7 36.9 1.0 CA A:ALA232 4.8 40.1 1.0 CG2 A:ILE262 4.8 33.5 1.0 CD2 A:LEU234 4.8 40.4 1.0 O A:CYS261 4.9 38.4 1.0 C A:ALA232 4.9 43.1 1.0 CA A:PHE219 4.9 34.2 1.0 N A:PHE263 5.0 34.2 1.0

F.Wang, K.O.Jeon, J.M.Salovich, J.D.Macdonald, J.Alvarado, R.D.Gogliotti, J.Phan, E.T.Olejniczak, Q.Sun, S.Wang, D.Camper, J.P.Yuh, J.G.Shaw, J.Sai, O.W.Rossanese, W.P.Tansey, S.R.Stauffer, S.W.Fesik. Discovery of Potent 2-Aryl-6,7-Dihydro-5 H-Pyrrolo[1,2- A]Imidazoles As WDR5-Win-Site Inhibitors Using Fragment-Based Methods and Structure-Based Design. J. Med. Chem. V. 61 5623 2018.
ISSN: ISSN 1520-4804
PubMed: 29889518
DOI: 10.1021/ACS.JMEDCHEM.8B00375