Sodium in PDB 7jxx: Structure of TTBK1 Kinase Domain in Complex with Compound 3

All present enzymatic activity of Structure of TTBK1 Kinase Domain in Complex with Compound 3:
2.7.11.1;

The structure of Structure of TTBK1 Kinase Domain in Complex with Compound 3, PDB code: 7jxx was solved by J.V.Chodaprambil, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.40 / 1.56
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	173.837, 34.337, 48.666, 90, 103.5, 90
R / Rfree (%)	18 / 21.3

The binding sites of Sodium atom in the Structure of TTBK1 Kinase Domain in Complex with Compound 3 (pdb code 7jxx). 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 TTBK1 Kinase Domain in Complex with Compound 3, PDB code: 7jxx:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Structure of TTBK1 Kinase Domain in Complex with Compound 3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of TTBK1 Kinase Domain in Complex with Compound 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:21.2 occ:1.00 O A:HOH636 2.9 20.7 1.0 O A:HOH748 3.5 39.3 1.0 CA A:GLY111 4.0 19.5 1.0 CG A:ARG112 4.0 25.7 1.0 NE A:ARG112 4.1 23.3 1.0 N A:ARG112 4.3 17.3 1.0 CD A:ARG112 4.3 25.0 1.0 CB A:ARG164 4.3 19.4 1.0 C A:GLY111 4.6 16.9 1.0 CZ A:ARG112 4.8 27.6 1.0

Sodium binding site 2 out of 3 in the Structure of TTBK1 Kinase Domain in Complex with Compound 3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of TTBK1 Kinase Domain in Complex with Compound 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:63.2 occ:1.00 O A:HOH624 3.0 29.2 1.0 O A:HOH631 3.5 41.8 1.0 NE A:ARG57 4.7 22.2 1.0 NH2 A:ARG57 4.8 26.9 1.0 CB A:ARG57 4.9 20.8 1.0 O A:HOH765 4.9 52.8 1.0

Sodium binding site 3 out of 3 in the Structure of TTBK1 Kinase Domain in Complex with Compound 3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of TTBK1 Kinase Domain in Complex with Compound 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:26.1 occ:1.00 OG1 A:THR168 2.7 21.4 1.0 OE1 A:GLN110 2.7 23.4 1.0 O A:HOH581 2.8 19.9 1.0 N A:ARG164 2.9 22.6 1.0 CA A:GLY163 3.4 16.8 1.0 CB A:THR168 3.6 20.4 1.0 NE2 A:GLN108 3.6 20.2 1.0 C A:GLY163 3.6 24.6 1.0 CD A:GLN110 3.7 19.9 1.0 CG A:ARG164 3.8 22.2 1.0 CG A:LEU165 3.8 22.0 1.0 CA A:ARG164 4.0 19.8 1.0 N A:LEU165 4.0 20.1 1.0 CG2 A:THR168 4.0 25.5 1.0 CD1 A:LEU165 4.0 25.1 1.0 O A:LEU109 4.0 20.5 1.0 NE2 A:GLN110 4.1 18.0 1.0 C A:ARG164 4.2 16.6 1.0 CB A:ARG164 4.4 19.4 1.0 CB A:LEU165 4.5 21.6 1.0 CD A:GLN108 4.6 24.2 1.0 CE1 A:TYR173 4.6 21.6 1.0 N A:GLY163 4.7 15.7 1.0 CA A:GLN110 4.7 15.2 1.0 O A:GLY163 4.8 19.1 1.0 CA A:LEU165 4.8 19.3 1.0 CD A:ARG164 4.9 28.1 1.0 CZ A:TYR173 4.9 23.5 1.0 CG A:GLN108 4.9 20.8 1.0 OH A:TYR173 4.9 26.5 1.0 CA A:THR168 4.9 21.0 1.0

T.Halkina, J.L.Henderson, E.Y.Lin, M.K.Himmelbauer, J.H.Jones, M.Nevalainen, J.Feng, K.King, M.Rooney, J.L.Johnson, D.J.Marcotte, J.V.Chodaparambil, P.R.Kumar, T.A.Patterson, P.Murugan, E.Schuman, L.Wong, T.Hesson, S.Lamore, C.Bao, M.Calhoun, H.Certo, B.Amaral, G.M.Dillon, R.Gilfillan, F.G.De Turiso. Discovery of Potent and Brain-Penetrant Tau Tubulin Kinase 1 (TTBK1) Inhibitors That Lower Tau Phosphorylation in Vivo. J.Med.Chem. 2021.
ISSN: ISSN 0022-2623
PubMed: 33944571
DOI: 10.1021/ACS.JMEDCHEM.1C00382