Sodium in PDB 7ack: CDK2/Cyclin A2 in Complex with An Imidazo[1,2-C]Pyrimidin-5-One Inhibitor

All present enzymatic activity of CDK2/Cyclin A2 in Complex with An Imidazo[1,2-C]Pyrimidin-5-One Inhibitor:
2.7.11.22;

The structure of CDK2/Cyclin A2 in Complex with An Imidazo[1,2-C]Pyrimidin-5-One Inhibitor, PDB code: 7ack was solved by J.Skerlova, P.Pachl, P.Rezacova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.16 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	71.305, 163.451, 73.19, 90, 106.18, 90
R / Rfree (%)	19.7 / 23.2

The binding sites of Sodium atom in the CDK2/Cyclin A2 in Complex with An Imidazo[1,2-C]Pyrimidin-5-One Inhibitor (pdb code 7ack). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the CDK2/Cyclin A2 in Complex with An Imidazo[1,2-C]Pyrimidin-5-One Inhibitor, PDB code: 7ack:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the CDK2/Cyclin A2 in Complex with An Imidazo[1,2-C]Pyrimidin-5-One Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of CDK2/Cyclin A2 in Complex with An Imidazo[1,2-C]Pyrimidin-5-One Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Na505 b:28.9 occ:1.00 O B:HOH752 2.4 61.3 1.0 O B:GLN203 2.6 37.7 1.0 O B:HOH776 2.6 55.9 1.0 O B:MET200 2.6 36.4 1.0 O B:ILE206 2.7 35.3 1.0 O B:HOH726 3.0 44.4 1.0 C B:GLN203 3.7 36.3 1.0 C B:MET200 3.8 35.2 1.0 C B:ILE206 3.9 33.8 1.0 CB B:GLN203 4.2 34.2 1.0 CA B:GLN203 4.4 34.5 1.0 N B:GLN203 4.4 37.4 1.0 CG B:MET200 4.4 33.3 1.0 CA B:LYS201 4.4 42.3 1.0 O B:LYS201 4.4 44.6 1.0 C B:LYS201 4.5 42.9 1.0 N B:LYS201 4.5 36.0 1.0 CA B:THR207 4.6 30.8 1.0 N B:ILE206 4.6 35.5 1.0 N B:THR207 4.7 30.7 1.0 O B:PRO204 4.7 43.1 1.0 C B:PRO204 4.7 41.8 1.0 CG2 B:THR207 4.7 32.1 1.0 O B:HOH718 4.8 38.5 1.0 CA B:MET200 4.8 36.5 1.0 N B:PRO204 4.8 40.5 1.0 SD B:MET200 4.9 36.5 1.0 CA B:ILE206 4.9 35.8 1.0 CA B:PRO204 4.9 41.8 1.0

Sodium binding site 2 out of 2 in the CDK2/Cyclin A2 in Complex with An Imidazo[1,2-C]Pyrimidin-5-One Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of CDK2/Cyclin A2 in Complex with An Imidazo[1,2-C]Pyrimidin-5-One Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ D:Na505 b:29.9 occ:1.00 O D:HOH740 2.4 53.2 1.0 O D:HOH714 2.5 43.8 1.0 O D:GLN203 2.6 43.0 1.0 O D:ILE206 2.6 39.0 1.0 O D:MET200 2.8 39.1 1.0 O D:HOH687 2.9 55.9 1.0 C D:GLN203 3.7 38.9 1.0 C D:ILE206 3.8 37.9 1.0 C D:MET200 3.9 37.2 1.0 CB D:GLN203 4.2 37.4 1.0 CA D:GLN203 4.4 37.7 1.0 N D:GLN203 4.4 40.2 1.0 CG D:MET200 4.4 37.9 1.0 N D:ILE206 4.4 37.4 1.0 O D:LYS201 4.4 52.3 1.0 CA D:LYS201 4.5 48.9 1.0 O D:PRO204 4.5 45.2 1.0 CA D:THR207 4.6 33.3 1.0 C D:LYS201 4.6 47.8 1.0 C D:PRO204 4.6 44.8 1.0 N D:LYS201 4.6 41.2 1.0 N D:THR207 4.6 36.0 1.0 O D:HOH703 4.6 43.8 1.0 CG2 D:THR207 4.7 36.9 1.0 CA D:ILE206 4.7 39.7 1.0 N D:PRO204 4.8 42.2 1.0 SD D:MET200 4.8 39.8 1.0 CA D:MET200 4.9 37.0 1.0 CA D:PRO204 4.9 44.7 1.0 N D:ASP205 4.9 42.9 1.0

J.Jansa, R.Jorda, J.Skerlova, P.Pachl, M.Perina, E.Reznickova, T.Heger, T.Gucky, P.Rezacova, A.Lycka, V.Krystof. Imidazo[1,2-C]Pyrimidin-5(6H)-One Inhibitors of CDK2: Synthesis, Kinase Inhibition and Co-Crystal Structure. Eur.J.Med.Chem. V. 216 13309 2021.
ISSN: ISSN 0223-5234
PubMed: 33711765
DOI: 10.1016/J.EJMECH.2021.113309