Magnesium in PDB 5fp3: Cell Penetrant Inhibitors of the JMJD2 (KDM4) and JARID1 (KDM5) Families of Histone Lysine Demethylases

The structure of Cell Penetrant Inhibitors of the JMJD2 (KDM4) and JARID1 (KDM5) Families of Histone Lysine Demethylases, PDB code: 5fp3 was solved by C.Chung, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	71.30 / 2.05
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	61.199, 65.552, 77.301, 85.59, 67.65, 68.39
R / Rfree (%)	20.5 / 24.3

The structure of Cell Penetrant Inhibitors of the JMJD2 (KDM4) and JARID1 (KDM5) Families of Histone Lysine Demethylases also contains other interesting chemical elements:

Cobalt	(Co)	2 atoms
Zinc	(Zn)	2 atoms

The binding sites of Magnesium atom in the Cell Penetrant Inhibitors of the JMJD2 (KDM4) and JARID1 (KDM5) Families of Histone Lysine Demethylases (pdb code 5fp3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Cell Penetrant Inhibitors of the JMJD2 (KDM4) and JARID1 (KDM5) Families of Histone Lysine Demethylases, PDB code: 5fp3:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Cell Penetrant Inhibitors of the JMJD2 (KDM4) and JARID1 (KDM5) Families of Histone Lysine Demethylases


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cell Penetrant Inhibitors of the JMJD2 (KDM4) and JARID1 (KDM5) Families of Histone Lysine Demethylases within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2639 b:46.7 occ:1.00 O A:HOH2247 2.0 33.5 1.0 O A:HOH2248 2.0 44.0 1.0 O A:HOH2295 2.3 48.7 1.0 O A:HOH2458 2.4 41.2 1.0 O A:HOH2291 2.6 43.8 1.0 O A:HOH2459 2.9 45.7 1.0 OE2 A:GLU1498 3.2 29.9 1.0 OE2 A:GLU1415 3.2 24.9 1.0 O A:HOH2245 3.2 30.5 1.0 OE1 A:GLU1415 3.7 24.4 1.0 CD A:GLU1415 3.9 24.0 1.0 CD A:GLU1498 4.2 28.4 1.0 O A:HOH2296 4.3 42.7 1.0 OE1 A:GLU1498 4.5 29.1 1.0 CD2 A:LEU1495 4.5 21.9 1.0 O A:HOH2250 4.6 29.9 1.0 NE1 A:TRP1418 4.9 24.4 1.0 O A:HOH2231 5.0 27.1 1.0

Magnesium binding site 2 out of 4 in the Cell Penetrant Inhibitors of the JMJD2 (KDM4) and JARID1 (KDM5) Families of Histone Lysine Demethylases


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cell Penetrant Inhibitors of the JMJD2 (KDM4) and JARID1 (KDM5) Families of Histone Lysine Demethylases within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2642 b:24.2 occ:1.00 O6 A:BCN2640 2.3 28.8 0.5 O4 A:BCN2641 2.4 35.5 1.0 O6 A:BCN2641 2.4 35.1 1.0 O21 A:BCN2640 2.4 31.3 0.5 O21 A:BCN2641 2.5 33.2 1.0 O4 A:BCN2640 2.5 26.9 0.5 N1 A:BCN2641 2.7 33.6 1.0 O21 A:BCN2640 2.7 27.9 0.5 N1 A:BCN2640 2.7 27.1 0.5 N1 A:BCN2640 2.8 29.8 0.5 O6 A:BCN2640 3.0 26.0 0.5 C4 A:BCN2641 3.2 34.3 1.0 C2 A:BCN2641 3.2 33.8 1.0 C6 A:BCN2640 3.2 28.8 0.5 C6 A:BCN2640 3.3 26.0 0.5 C2 A:BCN2640 3.3 27.7 0.5 C2 A:BCN2640 3.3 30.6 0.5 C4 A:BCN2640 3.3 27.2 0.5 C5 A:BCN2641 3.4 34.0 1.0 C6 A:BCN2641 3.4 34.2 1.0 C5 A:BCN2640 3.4 29.0 0.5 C1 A:BCN2641 3.4 33.1 1.0 C5 A:BCN2640 3.4 26.4 0.5 C3 A:BCN2641 3.5 33.8 1.0 C3 A:BCN2640 3.5 27.3 0.5 C1 A:BCN2640 3.5 27.4 0.5 C1 A:BCN2640 3.6 30.2 0.5 C4 A:BCN2640 3.7 29.5 0.5 C3 A:BCN2640 3.8 29.7 0.5 O22 A:BCN2640 4.2 28.2 0.5 O22 A:BCN2641 4.3 34.6 1.0 O4 A:BCN2640 4.3 29.6 0.5 O22 A:BCN2640 4.5 30.9 0.5 O3 A:YC81 4.6 21.8 1.0

Magnesium binding site 3 out of 4 in the Cell Penetrant Inhibitors of the JMJD2 (KDM4) and JARID1 (KDM5) Families of Histone Lysine Demethylases


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cell Penetrant Inhibitors of the JMJD2 (KDM4) and JARID1 (KDM5) Families of Histone Lysine Demethylases within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2639 b:48.9 occ:1.00 O B:HOH2347 2.0 37.5 1.0 O B:HOH2187 2.3 36.4 1.0 O B:HOH2345 2.6 44.7 1.0 O B:HOH2346 2.6 40.1 1.0 O B:HOH2232 2.8 36.1 1.0 O B:HOH2188 2.9 37.4 1.0 OE2 B:GLU1415 3.0 22.4 1.0 OE1 B:GLU1498 3.5 27.4 1.0 OE1 B:GLU1415 3.5 22.4 1.0 O B:HOH2193 3.6 30.2 1.0 CD B:GLU1415 3.6 21.8 1.0 CD2 B:LEU1495 4.2 21.5 1.0 OE2 B:GLU1498 4.2 28.2 1.0 CD B:GLU1498 4.3 26.9 1.0 NE1 B:TRP1418 4.7 23.3 1.0 O B:HOH2190 4.8 30.6 1.0 O B:HOH2189 4.9 24.5 1.0

Magnesium binding site 4 out of 4 in the Cell Penetrant Inhibitors of the JMJD2 (KDM4) and JARID1 (KDM5) Families of Histone Lysine Demethylases


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cell Penetrant Inhibitors of the JMJD2 (KDM4) and JARID1 (KDM5) Families of Histone Lysine Demethylases within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2642 b:20.9 occ:1.00 O4 B:BCN2640 2.3 36.9 1.0 O22 B:BCN2640 2.3 36.8 1.0 O6 B:BCN2641 2.4 26.8 1.0 O4 B:BCN2641 2.4 29.4 1.0 O22 B:BCN2641 2.5 31.1 1.0 O6 B:BCN2640 2.5 31.8 1.0 N1 B:BCN2640 2.7 33.6 1.0 N1 B:BCN2641 2.7 28.5 1.0 C6 B:BCN2641 3.1 26.4 1.0 C2 B:BCN2640 3.3 36.4 1.0 C6 B:BCN2640 3.4 31.7 1.0 C3 B:BCN2641 3.4 28.3 1.0 C4 B:BCN2640 3.4 35.2 1.0 C4 B:BCN2641 3.4 28.3 1.0 C3 B:BCN2640 3.4 34.3 1.0 C2 B:BCN2641 3.4 30.9 1.0 C5 B:BCN2640 3.4 32.1 1.0 C5 B:BCN2641 3.4 27.4 1.0 C1 B:BCN2640 3.5 34.7 1.0 C1 B:BCN2641 3.7 29.7 1.0 O B:HOH2172 4.0 34.0 1.0 O21 B:BCN2640 4.4 37.5 1.0 O B:HOH2205 4.5 27.5 1.0 O21 B:BCN2641 4.6 33.5 1.0 O3 B:YC81 4.6 22.4 1.0

S.M.Westaway, A.G.S.Preston, M.D.Barker, F.Brown, J.A.Brown, M.Campbell, C.Chung, H.Diallo, C.Douault, G.Drewes, R.Eagle, L.Gordon, C.Haslam, T.G.Hayhow, P.G.Humphreys, G.Joberty, R.Katso, L.Kruidenier, M.Leveridge, J.Liddle, J.Mosley, M.Muelbaier, R.Randle, I.Rioja, A.Rueger, G.A.Seal, R.J.Sheppard, O.Singh, J.Taylor, P.Thomas, D.Thomson, D.M.Wilson, K.Lee, R.K.Prinjha. Cell Penetrant Inhibitors of the KDM4 and KDM5 Families of Histone Lysine Demethylases. 1. 3-Amino-4-Pyridine Carboxylate Derivatives. J.Med.Chem. V. 59 1357 2016.
ISSN: ISSN 0022-2623
PubMed: 26771107
DOI: 10.1021/ACS.JMEDCHEM.5B01537