Sodium in PDB 7rsv: Structure of the VPS34 Kinase Domain with Compound 5

All present enzymatic activity of Structure of the VPS34 Kinase Domain with Compound 5:
2.7.1.137;

The structure of Structure of the VPS34 Kinase Domain with Compound 5, PDB code: 7rsv 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)	34.50 / 1.78
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.706, 119.027, 91.287, 90, 108.95, 90
R / Rfree (%)	17.9 / 21.4

The binding sites of Sodium atom in the Structure of the VPS34 Kinase Domain with Compound 5 (pdb code 7rsv). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Structure of the VPS34 Kinase Domain with Compound 5, PDB code: 7rsv:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Structure of the VPS34 Kinase Domain with Compound 5


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 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na904 b:62.2 occ:1.00 OD1 A:ASP409 3.0 51.7 1.0 OD2 A:ASP409 3.1 55.7 1.0 CG A:ASP409 3.4 44.7 1.0 O A:HOH1275 4.4 51.0 1.0 O A:HOH1406 4.6 49.1 1.0 CB A:ASP409 4.9 35.6 1.0

Sodium binding site 2 out of 5 in the Structure of the VPS34 Kinase Domain with Compound 5


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 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na905 b:60.6 occ:1.00 CB A:HIS637 3.5 36.3 1.0 ND1 A:HIS637 3.6 63.8 1.0 O A:HIS637 3.6 35.8 1.0 O A:LEU616 3.8 31.8 1.0 CG A:GLN560 3.8 63.5 1.0 O A:HOH1201 4.0 35.4 1.0 CG A:HIS637 4.0 58.0 1.0 O A:MET617 4.1 31.2 1.0 C A:HIS637 4.2 34.9 1.0 CA A:HIS637 4.3 28.7 1.0 CB A:MET556 4.5 34.0 1.0 N A:HIS637 4.5 26.5 1.0 CD A:GLN560 4.6 71.8 1.0 O A:MET556 4.7 41.1 1.0 NE2 A:GLN560 4.7 77.6 1.0 C A:MET617 4.8 33.8 1.0 CE1 A:HIS637 4.8 65.4 1.0 SD A:MET556 4.9 50.1 1.0 CB A:GLN560 4.9 59.2 1.0 C A:LEU616 5.0 30.5 1.0

Sodium binding site 3 out of 5 in the Structure of the VPS34 Kinase Domain with Compound 5


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 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na906 b:70.3 occ:1.00 OG1 A:THR610 3.7 36.2 1.0 O A:HOH1325 3.7 56.1 1.0 NE2 A:GLN620 4.0 31.7 1.0 CE2 A:PHE612 4.2 34.7 1.0 CD2 A:PHE612 4.2 33.4 1.0 CZ A:PHE612 4.4 37.9 1.0 CG A:PHE612 4.5 27.0 1.0 O A:LEU611 4.5 29.9 1.0 O A:HOH1002 4.6 37.1 1.0 CA A:PHE612 4.6 29.1 1.0 CD A:GLN620 4.6 37.0 1.0 CB A:GLN620 4.6 30.4 1.0 CB A:THR610 4.7 38.0 1.0 CE1 A:PHE612 4.7 25.8 1.0 CD1 A:PHE612 4.7 26.2 1.0 C A:LEU611 4.8 29.3 1.0 N A:PHE612 4.8 30.6 1.0

Sodium binding site 4 out of 5 in the Structure of the VPS34 Kinase Domain with Compound 5


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of the VPS34 Kinase Domain with Compound 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na907 b:58.4 occ:1.00 O A:HOH1178 3.4 48.4 1.0 O A:HOH1182 3.8 40.4 1.0 CG2 A:THR668 4.0 22.2 1.0 CA A:THR668 4.1 24.7 1.0 CD A:PRO669 4.3 24.6 1.0 O A:HOH1393 4.3 50.4 1.0 CD1 A:ILE685 4.4 23.5 1.0 N A:PRO669 4.4 23.9 1.0 C A:THR668 4.5 22.9 1.0 O A:LEU667 4.6 22.8 1.0 CB A:THR668 4.6 22.1 1.0 C A:PRO669 4.8 28.3 1.0 O A:PRO669 4.9 25.3 1.0 OG1 A:THR668 4.9 23.8 1.0 N A:TYR670 5.0 21.7 1.0 CG A:PRO669 5.0 29.2 1.0

Sodium binding site 5 out of 5 in the Structure of the VPS34 Kinase Domain with Compound 5


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of the VPS34 Kinase Domain with Compound 5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na903 b:62.1 occ:1.00 OH B:TYR496 3.9 28.7 1.0 CZ B:TYR492 4.1 30.7 1.0 CE1 B:TYR492 4.1 30.1 1.0 CG B:LEU393 4.2 43.1 1.0 CE B:MET394 4.2 23.9 0.4 O B:HOH1160 4.2 40.1 1.0 CD2 B:LEU393 4.2 48.9 1.0 O B:HOH1151 4.3 31.6 1.0 CE2 B:TYR492 4.4 24.2 1.0 O B:LEU393 4.4 23.1 1.0 OH B:TYR492 4.4 31.7 1.0 CD1 B:TYR492 4.5 26.6 1.0 CD2 B:TYR492 4.7 24.8 1.0 CD1 B:LEU393 4.7 43.4 1.0 CG B:TYR492 4.8 22.2 1.0 O B:HOH1280 4.9 38.2 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