Sodium in PDB 7rsj: Structure of the VPS34 Kinase Domain with Compound 14

All present enzymatic activity of Structure of the VPS34 Kinase Domain with Compound 14:
2.7.1.137;

The structure of Structure of the VPS34 Kinase Domain with Compound 14, PDB code: 7rsj was solved by D.X.Hu, S.Patel, H.Chen, S.Wang, S.Staben, Y.N.Dimitrova, H.A.Wallweber, J.Y.Lee, G.K.Y.Chan, C.J.Sneeringer, M.S.Prangley, J.G.Moffat, C.Wu, L.K.Schutt, L.Salphati, J.Pang, E.Mcnamara, H.Huang, Y.Chen, Y.Wang, W.Zhao, J.Lim, A.Murthy, M.Siu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	77.01 / 1.88
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.302, 107.386, 110.502, 90, 90, 90
R / Rfree (%)	16.8 / 20.3

The binding sites of Sodium atom in the Structure of the VPS34 Kinase Domain with Compound 14 (pdb code 7rsj). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Structure of the VPS34 Kinase Domain with Compound 14, PDB code: 7rsj:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Structure of the VPS34 Kinase Domain with Compound 14


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the VPS34 Kinase Domain with Compound 14 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na901 b:45.3 occ:1.00 O A:ILE605 2.7 32.5 1.0 OG1 A:THR608 2.7 30.2 1.0 N A:PHE622 2.9 28.3 1.0 N A:ALA609 3.2 30.5 1.0 C A:THR608 3.3 35.6 1.0 CA A:ALA609 3.5 31.4 1.0 CB A:PHE622 3.6 28.7 1.0 CD1 A:PHE622 3.6 32.8 1.0 CB A:ALA609 3.7 30.0 1.0 CA A:PHE622 3.7 32.5 1.0 O A:THR608 3.7 34.1 1.0 CB A:THR608 3.7 35.1 1.0 C A:ILE605 3.8 34.6 1.0 O A:PHE622 3.8 30.3 1.0 C A:LEU621 3.8 30.8 1.0 CA A:LEU621 3.9 28.1 1.0 CA A:THR608 3.9 32.4 1.0 CG2 A:ILE604 4.0 28.9 1.0 N A:THR608 4.0 33.8 1.0 CB A:ILE605 4.0 32.2 1.0 CG A:PHE622 4.1 28.8 1.0 N A:ILE605 4.2 31.4 1.0 C A:PHE622 4.2 33.6 1.0 CA A:ILE605 4.2 33.3 1.0 O A:GLN620 4.5 29.9 1.0 CG2 A:ILE605 4.6 35.5 1.0 O A:HOH1058 4.7 35.2 1.0 CE1 A:PHE622 4.7 33.0 1.0 CB A:LEU621 4.8 28.5 1.0 O A:PRO606 4.9 37.5 1.0 N A:LEU621 4.9 28.1 1.0 N A:PRO606 4.9 31.7 1.0 C A:PRO606 4.9 40.6 1.0

Sodium binding site 2 out of 3 in the Structure of the VPS34 Kinase Domain with Compound 14


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the VPS34 Kinase Domain with Compound 14 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na902 b:59.9 occ:1.00 NH1 A:ARG482 3.1 35.8 1.0 NH1 A:ARG385 3.3 81.1 1.0 CG A:ARG385 3.4 59.7 1.0 CD A:ARG482 3.8 37.3 1.0 CD A:ARG385 3.9 69.3 1.0 CZ A:ARG482 4.0 38.9 1.0 NZ A:LYS485 4.2 79.0 1.0 O A:ARG385 4.2 39.7 1.0 NE A:ARG482 4.3 38.4 1.0 CZ A:ARG385 4.3 73.6 1.0 CB A:ARG385 4.5 41.0 1.0 CE1 A:PHE478 4.5 35.2 1.0 NE A:ARG385 4.5 73.3 1.0 CG A:ARG482 4.8 33.1 1.0

Sodium binding site 3 out of 3 in the Structure of the VPS34 Kinase Domain with Compound 14


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of the VPS34 Kinase Domain with Compound 14 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na903 b:63.9 occ:1.00 CE1 A:TYR812 3.9 43.1 1.0 O A:ARG811 4.1 33.4 1.0 CZ A:TYR812 4.1 49.3 1.0 OH A:TYR812 4.3 55.0 1.0 CD1 A:TYR812 4.4 40.9 1.0 CB A:ARG811 4.7 42.4 1.0 CE2 A:TYR812 4.8 40.8 1.0 C A:ARG811 4.8 35.0 1.0

D.X.Hu, S.Patel, H.Chen, S.Wang, S.T.Staben, Y.N.Dimitrova, H.A.Wallweber, J.Y.Lee, G.K.Y.Chan, C.J.Sneeringer, M.S.Prangley, J.G.Moffat, K.C.Wu, L.K.Schutt, L.Salphati, J.Pang, E.Mcnamara, H.Huang, Y.Chen, Y.Wang, W.Zhao, J.Lim, A.Murthy, M.Siu. Structure-Based Design of Potent, Selective, and Orally Bioavailable VPS34 Kinase Inhibitors. J.Med.Chem. 2021.
ISSN: ISSN 0022-2623
PubMed: 34779204
DOI: 10.1021/ACS.JMEDCHEM.1C01180