Zinc in PDB 5kr7: KDM4C Bound to Pyrazolo-Pyrimidine Scaffold

The structure of KDM4C Bound to Pyrazolo-Pyrimidine Scaffold, PDB code: 5kr7 was solved by S.F.Bellon, F.Poy, J.W.Setser, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	66.82 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	89.817, 89.876, 100.011, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 23.4

The structure of KDM4C Bound to Pyrazolo-Pyrimidine Scaffold also contains other interesting chemical elements:

Iron	(Fe)	2 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Zinc atom in the KDM4C Bound to Pyrazolo-Pyrimidine Scaffold (pdb code 5kr7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the KDM4C Bound to Pyrazolo-Pyrimidine Scaffold, PDB code: 5kr7:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the KDM4C Bound to Pyrazolo-Pyrimidine Scaffold


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of KDM4C Bound to Pyrazolo-Pyrimidine Scaffold within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:26.8 occ:1.00 NE2 A:HIS242 2.2 24.5 1.0 SG A:CYS236 2.3 25.1 1.0 SG A:CYS308 2.3 31.2 1.0 SG A:CYS310 2.3 41.5 1.0 CB A:CYS310 2.8 41.2 1.0 CD2 A:HIS242 3.1 25.0 1.0 CE1 A:HIS242 3.2 26.1 1.0 CB A:CYS308 3.2 30.4 1.0 CB A:CYS236 3.2 25.9 1.0 N A:CYS310 3.6 46.2 1.0 CA A:CYS310 3.8 47.2 1.0 CA A:CYS308 3.9 30.9 1.0 NE A:ARG311 3.9 65.3 1.0 N A:THR309 4.0 46.6 1.0 CD A:ARG311 4.0 69.6 1.0 C A:CYS308 4.2 38.7 1.0 ND1 A:HIS242 4.3 27.4 1.0 CG A:HIS242 4.3 26.2 1.0 CA A:CYS236 4.6 30.5 1.0 O A:ALA238 4.7 20.3 1.0 C A:THR309 4.7 56.0 1.0 N A:ARG311 4.8 52.5 1.0 CA A:PHE239 4.9 19.2 1.0 C A:CYS310 4.9 51.8 1.0 C A:ALA238 4.9 20.5 1.0 CA A:THR309 5.0 56.4 1.0

Zinc binding site 2 out of 2 in the KDM4C Bound to Pyrazolo-Pyrimidine Scaffold


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of KDM4C Bound to Pyrazolo-Pyrimidine Scaffold within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:26.6 occ:1.00 NE2 B:HIS242 2.1 25.1 1.0 SG B:CYS236 2.3 24.9 1.0 SG B:CYS308 2.3 33.9 1.0 SG B:CYS310 2.4 37.5 1.0 CE1 B:HIS242 3.1 26.8 1.0 CD2 B:HIS242 3.1 24.1 1.0 CB B:CYS236 3.2 27.1 1.0 CB B:CYS308 3.4 28.3 1.0 CB B:CYS310 3.5 43.6 1.0 N B:CYS310 3.7 46.7 1.0 CD B:ARG311 3.9 64.4 1.0 CA B:CYS308 3.9 30.9 1.0 CA B:CYS310 4.0 46.6 1.0 NE B:ARG311 4.1 70.8 1.0 N B:THR309 4.2 46.5 1.0 ND1 B:HIS242 4.2 26.1 1.0 CG B:HIS242 4.2 27.0 1.0 C B:CYS308 4.3 37.5 1.0 N B:ARG311 4.4 48.9 1.0 C B:CYS310 4.5 47.3 1.0 CA B:CYS236 4.6 31.4 1.0 O B:ALA238 4.8 19.0 1.0 C B:THR309 4.9 63.6 1.0 CA B:PHE239 5.0 19.7 1.0

V.S.Gehling, S.F.Bellon, J.C.Harmange, Y.Leblanc, F.Poy, S.Odate, S.Buker, F.Lan, S.Arora, K.E.Williamson, P.Sandy, R.T.Cummings, C.M.Bailey, L.Bergeron, W.Mao, A.Gustafson, Y.Liu, E.Vanderporten, J.E.Audia, P.Trojer, B.K.Albrecht. Identification of Potent, Selective KDM5 Inhibitors. Bioorg.Med.Chem.Lett. V. 26 4350 2016.
ISSN: ESSN 1464-3405
PubMed: 27476424
DOI: 10.1016/J.BMCL.2016.07.026